If I have some files I want to copy from my project into the .\\bin\\debug\\ folder on compilation, then it seems I have to put them into the root of the projec
You could do this with a post build event. Set the files to no action on compile, then in the macro copy the files to the directory you want.
Here's a post build Macro that I think will work by copying all files in a directory called Configuration to the root build folder:
copy $(ProjectDir)Configuration\* $(ProjectDir)$(OutDir)