Obviously I specify the location of the one in the MEP folder path. I'm wonding should I ever reach the state that my coded creations are set loose on my colleagues with Vanilla autocad, would there be a problem with the fact that the executables are in different locations?
It's probably a daft question, I'm still getting my head around how .Net works..
ACad, MEP, 3DS Max Windows 7x64 X5482 @3.2Ghz 8Gb Ram Quadro FX1700
As far as I understand your question, your users who use your .NET DLL in AutoCAD (vanilla or MEP, does not matter) do not have to be concerned about where the AutoCAD executable (acad.exe) is. The .NET dll can only run after being NETLOADED (or loading on demand) AFTER AutoCAD being already started. The DLL runs inside AutoCAD process.
The reason, that Acad plugin wizard in Visual studio asks you where the Acad executable is, is that it will let Visual Studio know how to start AutoCAD for debugging when you press F5. This has nothing to do with user using the .NET DLL your project produces.