I too am just about to get a HD for my KN6500. I can't claim to be any sort of expert, but what I'm going to do is:
Have 4 top level directories:
1. "Full" - Used for "full" files which will play by themselves. Of course one can always switch out different parts so that you can add your live input. If you ever want files that will just play, for example to listen to to get ideas, or to provide background music then it is useful to group these together.
2. "Backing" files - Which will contain part files, so that you have to add your lead part
3. "Style" files - Which will contain pure rythm styles
4. "Voices" files - Which will contain pure sound, effects etc. set-ups
Under each of these directories I'm going to have sub-directories sorted by the types of music I like to play. e.g. Slow Jazz, Ballad, Big Band etc. and under these will go the actual files.
This is my "starter for 10". I daresay it will all change later on, but it seems to follow how I actually structure my playing.
Hope this helps.
Keith