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How to call tool DLLs in C# when the DLL-path is different on the target PC?

I might be a bit stupid, but I want to create a tool in Visual Studio in C# and want to call third party tools via their API-DLLs. The only topics I found here are dealing with one of the two methods that I already know:
Compilation time: add a reference to "C:\FooTool\foo.dll" in my project + "using fooToolNamespace.fooToolClass" in my code (compilation time) --> I can "naturally" use the classes of the DLL and will even get full IntelliSense support if a suiting XML-file is available with the DLL. Also compilation time checks will be done for my usage of the dll.
Dynamic (run time): calling e.g. Assembly.LoadFile(#"C:\FooTool\foo.dll") and then using reflection on it to find functions, fields and so on --> no IntelliSense, no compilation time checks
So I actually have the DLL at hand and thus option 1) would be nice during development. But if my tool is used on a different PC, the third-party DLL might be in a different path there, e.g. "C:\foo\foo.dll" and "C:\bar\foo.dll".
In my understanding using a copy of "foo.dll" will not work, because "foo.dll" might have dependencies, e.g. requiring other files of the FooTool-directory. Thus in my understanding I have to call the DLL which is "installed" to the target PC and not a local copy of it.
So can I somehow change the path where my tool accesses the "foo.dll" at runtime and still use method 1) during development?
Or is there another way of doing things?
Or am I just dumb and there is a simple solution for all this?
Thanks a lot for the help and have a great day
Janis

To be able to use option 1 (a referenced DLL), you need to put the DLL somewhere "where your EXE (or, more precisely, the Assembly Resolver) can find it" on the customer's PC.
So where does the assembly resolver look for your DLL?
In the directory where the EXE resides (for desktop/console applications) or the bin subdirectory (for web applications). Since you mention that your DLL requires other dependencies as well, you'd need to copy them to that location as well.
The Global Assembly Cache (GAC). If your dependency supports this, installing it to the GAC ensures that it can be found by your application.
These two are the "supported" scenarios. There is also the possibility to tweak the assembly resolver to look into other directories as well, but that should be reserved for special cases where the other two options failed. (We had such a case and solved it with a custom AssemblyResolve handler on the application domain.)

Does GAC conflict with the Registry for Assembly Loading?

I have a DLL I generate from a C# project. I then register it via regasm so that the library can be used inside several legacy VB scripts.
Recently I created a new project (C# console app) that will reuse certain modular aspects of the original library, and per good programming practice it made sense to add the library to the GAC for reuse by this and any future projects.
I've found that it plays nice at first, but after the server is rebooted, the VB scripts crash and burn, claiming they are unable to create an object of one of the types defined in the library.
The fix involves removing the library from the GAC and re-registering the library via regasm.
The libraries in the registry and GAC come from the same physical DLL file - same directory and everything.
I've confirmed the existence of registry entries for the library every step of the way, which says regasm did its job.
GAC entries only exist when the library is installed, and properly disappear when it is uninstalled. They only ever appear under GAC_MSIL, where, to my knowledge, they should be.
Any ideas why this is happening?
EDIT: I did not read the fine print, haha. On the regasm documentation I just saw this: "Creates a Codebase entry in the registry. The Codebase entry specifies the file path for an assembly that's not installed in the global assembly cache. Don't specify this option if you will subsequently install the assembly that you're registering into the global assembly cache. It is strongly recommended the assemblyFile argument that you specify with the /codebase option be a strong-named assembly." I was using that switch, so I will dig deeper. In the meantime any additional insights are greatly appreciated.

I would guess you didn't renew the GUIDs and/or distinguish the fully qualified type names of the new library and when you installed it with regasm, the old entries in the registry got overwritten. Registering the old library again has overwritten the new library's registry, but as you don't use it through COM that didn't affect it and now the scripts work again.

Which assembly executes the code?

I'm working on a .net project, which is using third party .net DLLs. Some of this DLLs are using common DLLs (e.g. Microsoft.Practices.EnterpriseLibrary.Logging). Now we want to use the same common DLLs in a newer version. We are not allowed to use the GAC (politics).
We have separated the parts in different directories.
Third party \ Third party.dll
old common (Microsoft.Practices.EnterpriseLibrary.Logging.dll)
Our libs \ our lib.dll
new common (Microsoft.Practices.EnterpriseLibrary.Logging.dll)
Surprise, Surprise, it did not work. In our dll an error is thrown saying, some option is not valid. Yes, I did not find it in the old common, but in the new. So, I guess, the wrong executable was taken.
In Visual Studio (2015) we have enabled the "Spezific Version" in the reference, and in the Debug / module windows, both DLLs are loaded.
Edit: All Dlls have strong names.
How do I determine which DLL was executed (stepping with F11 just jump to the catch block)? How do I force using the correct DLL?
(The architecture loads first the third party DLL, then our own dll. This is not changeable without a few years rewriting...)

You can use assembly binding redirects and hope the universe doesn't break (there's no guarantee the newer DLL is backward compatible) or you can strong name the dlls.
Why? .NET generally does not allow you to load the "same" assembly more than once in the same AppDomain, unless it is strong-named. What's strong naming? It is a form of identity and digital signing that consists of:
Assembly filename
Assembly version
Assembly culture
Assembly public key
When it's strong-named, both dlls run side-by-side in the same AppDomain within the same process with perfect backward compatibility.
Alternatively if you don't want to use strong-naming (because many files may require signing) or binding redirects, you can always create additional AppDomains and load a version of the dlls into each domain.
Though it gets around the problem of fiddling with files, it does require considerable rework of the rest of the app making it an arguably bad choice at this point in your development.
EDIT: I see now you are using strong names on both.
How do I force using the correct DLL
To distinguish between the two types in the exact same namespace, you might have to create an alias for the newer assembly in your dll reference. Tell me more...

Strongly signed assemblies

I am not a .NET developer, so there might be some basic things I don't know.
I have some experience coding in C#, but now I have a question. One of my projects (A) references another ptoject (B), with "local copy" set. When B.dll is in the same location as A.exe everything works. But when B.dll is put in a common directory from PATH it doesn't work.
One of my coworkers said he thought I should make B strongly signed. Is he correct? Is that why one would strongly sign an assembly?
I read a bit about in in the internet but all I saw was about security... If so, how does one sign an assembly and what consequences does it have? Please note that I am using VS2003 .Net 1.1.
Edit: Thank you all very much for your answers, however all the links you provided refer to later versions of VS and .NET which have some sort of Signing tab in project properties. Does anybody know (or give a link )how to strongly name the assembly in VS2003 .Net1.1?

Your problem is not related to assembly signing in the first place. .NET does not use the PATH environment variable to load assemblies. The process is actually a bit more complex and you best read all details in MSDN (also see steps 1 to 4):
How the Runtime Locates Assemblies
In your case it might be the best to install the shared assembly to the GAC. Installing to the GAC requires that your assembly has a strong name, so this is probably what your co-worker referred to.
Update:
As you asked specifically about strong-naming a .NET 1.1 assembly I'd suggest checking out the following question:
How to give a .NET 1.1 dll a strong name in VS2003

I think that what your co-worker might be referring to is "Strong Naming" an Assembly.
Strong Naming is what enables you to deploy your assembly to the GAC.
Once it is in the GAC, then any application using that assembly can always locate it. Path's are irrelevant and that is the preferred way to have shared assemblies deployed.
To strong name an assembly, you can use the sn.exe tool that comes with Visual Studio to generate a strong name and then sign the assembly using the keyfile that is generated via sn.exe.
EDIT : Example of how to use SN.exe to strong name an assembly is here
Also, I think you should understand how the runtime loads assemblies. From MSDN
The runtime uses the following steps to resolve an assembly reference:
Determines the correct assembly version by examining applicable
configuration files, including the application configuration file,
publisher policy file, and machine configuration file.
If the configuration file is located on a remote machine, the
runtime must locate and download the application configuration file
first.
Checks whether the assembly name has been bound to before and, if so,
uses the previously loaded assembly.
Checks the global assembly cache. If the assembly is found there, the
runtime uses this assembly.
Probes for the assembly using the following steps: If configuration
and publisher policy do not affect the original reference and if the
bind request was created using the Assembly.LoadFrom method, the
runtime checks for location hints.
If a codebase is found in the configuration files, the runtime checks
only this location. If this probe fails, the runtime determines that
the binding request failed and no other probing occurs.
Probes for the assembly using the heuristics described in the probing
section. If the assembly is not found after probing, the runtime
requests the Windows Installer to provide the assembly. This acts as
an install-on-demand feature.
Note: There is no version checking for assemblies without strong
names, nor does the runtime check in the global assembly cache for
assemblies without strong names.

The right way to do this is by deploying your .dll in the GAC. http://support.microsoft.com/kb/815808

what is the reason you want to put the B.dll in a common directory? is it because it can be used by a another program? if so adding it to the GAC is the best option. See this one

As 0xA3 already mentioned you should read the article at MSDN. But what is not so good explained in the article is the usage of the AssemblyResolve event. It will be thrown if the Framework didn't find the assembly at any place, givin you a chance to start a search on yourself (maybe in your common folder) and return the needed assembly.
An example on how to use this, can be found in my question here.

Embedding assemblies inside another assembly

If you create a class library that uses things from other assemblies, is it possible to embed those other assemblies inside the class library as some kind of resource?
I.e. instead of having MyAssembly.dll, SomeAssembly1.dll and SomeAssembly2.dll sitting on the file system, those other two files get bundled in to MyAssembly.dll and are usable in its code.
I'm also a little confused about why .NET assemblies are .dll files. Didn't this format exist before .NET? Are all .NET assemblies DLLs, but not all DLLs are .NET assemblies? Why do they use the same file format and/or file extension?

ILMerge does merge assemblies, which is nice, but sometimes not quite what you want. For example, when the assembly in question is a strongly-named assembly, and you don't have the key for it, then you cannot do ILMerge without breaking that signature. Which means you have to deploy multiple assemblies.
As an alternative to ilmerge, you can embed one or more assemblies as resources into your exe or DLL. Then, at runtime, when the assemblies are being loaded, you can extract the embedded assembly programmatically, and load and run it. It sounds tricky but there's just a little bit of boilerplate code.
To do it, embed an assembly, just as you would embed any other resource (image, translation file, data, etc). Then, set up an AssemblyResolver that gets called at runtime. It should be set up in the static constructor of the startup class. The code is very simple.
static NameOfStartupClassHere()
{
AppDomain.CurrentDomain.AssemblyResolve += new ResolveEventHandler(Resolver);
}
static System.Reflection.Assembly Resolver(object sender, ResolveEventArgs args)
{
Assembly a1 = Assembly.GetExecutingAssembly();
Stream s = a1.GetManifestResourceStream(args.Name);
byte[] block = new byte[s.Length];
s.Read(block, 0, block.Length);
Assembly a2 = Assembly.Load(block);
return a2;
}
The Name property on the ResolveEventArgs parameter is the name of the assembly to be resolved. This name refers to the resource, not to the filename. If you embed the file named "MyAssembly.dll", and call the embedded resource "Foo", then the name you want here is "Foo". But that would be confusing, so I suggest using the filename of the assembly for the name of the resource. If you have embedded and named your assembly properly, you can just call GetManifestResourceStream() with the assembly name and load the assembly that way. Very simple.
This works with multiple assemblies, just as nicely as with a single embedded assembly.
In a real app you're gonna want better error handling in that routine - like what if there is no stream by the given name? What happens if the Read fails? etc. But that's left for you to do.
In the rest of the application code, you use types from the assembly as normal.
When you build the app, you need to add a reference to the assembly in question, as you would normally. If you use the command-line tools, use the /r option in csc.exe; if you use Visual Studio, you'll need to "Add Reference..." in the popup menu on the project.
At runtime, assembly version-checking and verification works as usual.
The only difference is in distribution. When you deploy or distribute your app, you need not distribute the DLL for the embedded (and referenced) assembly. Just deploy the main assembly; there's no need to distribute the other assemblies because they're embedded into the main DLL or EXE.

Take a look at ILMerge for merging assemblies.
I'm also a little confused about why .NET assemblies are .dll files. Didn't this format exist before .NET?
Yes.
Are all .NET assemblies DLLs,
Either DLLs or EXE normally - but can also be netmodule.
but not all DLLs are .NET assemblies?
Correct.
Why do they use the same file format and/or file extension?
Why should it be any different - it serves the same purpose!

You can embed an assembly (or any file, actually) as a resource (and then use the ResourceManager class to access them), but if you just want to combine assemblies, you're better off using a tool like ILMerge.
EXE and DLL files are Windows portable executables, which are generic enough to accomodate future types of code, including any .NET code (they can also run in DOS but only display a message saying that they're not supposed to run in DOS). They include instructions to fire up the .NET runtime if it isn't already running. It's also possible for a single assembly to span across multiple files, though this is hardly ever the case.

Note ILMerge doesn't work with embedded resources like XAML, so WPF apps etc will need to use Cheeso's method.

There's also the mkbundle utility offered by the Mono project

Why do they use the same file format and/or file extension?
Why should it be any different - it serves the same purpose!
My 2¢ bit of clarification here: DLL is Dynamic Link Library. Both the old style .dll (C-code) and .net style .dll are by definition "dynamic link" libraries. So .dll is a proper description for both.

With respect to Cheeso's answer of embedding the assemblies as resources and loading them dynamically using the Load(byte[]) overload using an AssemblyResolve event handler, you need to modify the resolver to check the AppDomain for an existing instance of the Assembly to load and return the existing assembly instance if it's already loaded.
Assemblies loaded using that overload do not have a context, which can cause the framework to try and reload the assembly multiple times. Without returning an already loaded instance, you can end up with multiple instances of the same assembly code and types that should be equal but won't be, because the framework considers them to be from two different assemblies.
At least one way that multiple AssemblyResolve events will be made for the same assembly loaded into the "No context" is when you have references to types it exposes from multiple assemblies loaded into your AppDomain, as code executes that needs those types resolved.
https://msdn.microsoft.com/en-us/library/dd153782%28v=vs.110%29.aspx
A couple of salient points from the link:
"Other assemblies cannot bind to assemblies that are loaded without context, unless you handle the AppDomain.AssemblyResolve event"
"Loading multiple assemblies with the same identity without context can cause type identity problems similar to those caused by loading assemblies with the same identity into multiple contexts. See Avoid Loading an Assembly into Multiple Contexts."

I would suggest you to try Costura.Fody. Just don't forget to Install-Package Fody before Costura.Fody (in order to get the newest Fody!)