Good thinking ahead...
However - I think this is up to you - I don't think there is a set in stone anything here. Being Organized - like it looks like you want to be - is reall ythe most import thing. Find a structure that makes sense to you and stick with it.
Note - the Compiler makes the debug and release "dirs" under where your source code is - but when you run from the compiler - your "Source" directory is the current working directory.
This is an important thing to remember for when you try to run your exe out of the compiler. Simply copy the exe up to your source code directory (so when you launch it the working directory is what it was in the compiler... and you are smooth sailing.
Another thing I do - is I have a Archives Directory - Separate from my programming and "in progress media" that is just for 3d related stuff. I have a media directory, which breaks down into gfx, audi, source snippets, and breaks down even further in each of these... in gfx I have textures, terrain related, fonts, etc.
This is my piggy bank of stuff to copy to my coding area at will.... etc.
Hope this sparks an idea or two for ya.
