the compile option does not depend on your build system. It is important, what your projects contain and what target platform you want to support.
My suggestion would be to use AnyCPU. And if you run into trouble with that setting you have to read further on the topic on how to solve it (or simply come back and we will help on your problems. The core is, that you might want to add some platform specific
stuff inside your assemblies e.g. access to a 32Bit DLL which requires that you run your application as 32Bit!)