Thanks for the help guys.
At this point what I think I will do is create a separate project and just build two different dlls. That way i can add the correct reference for each project and use the same code. I am using the AutoLoader so it will only have to setup the PackageContents.xml file once. Plus I will create a batch file to move my newly built dlls into my build directory for the AutoLoader. It will take a few minutes to setup but when done will be easy to maintain.
Out of curiosity, is there any way to manipulate the support path using pure .net that does not involve using the registry? I was really trying to avoid going down that path.