Since the linux kernel is based on Makefiles, that's what you should be looking at. As someone else said above. I can't say much more without knowing what are you exactly doing and what exact changes did you do to the kernel source tree.
However, instead of modifying the well probed and studied kernel tree structure, I'd rather suggest you to copy the full tree to a given alternate location, and work on that separate tree, instead of doing overly complicated things or nesting trees like I think you are doing. That will also allow you to easily make a diff later if you want to make a patch.