I am working in android SDK(Eclipse) platform 2.2 and I have been running through some tutorials, and some of them say to just add files to existing folder, or add folders; with
If you are using eclipse, have you tried right clicking on the /res folder and selecting "refresh" (or pressing F5). R.java should only ever be automatically generated and not edited manually.
Also, I'm not certain if this is what you're asking, but you cannot place further sub-directories within any of the /res directories.