I have the bestest suggestion possible:
1) Organize your ebooks in a "library" on your computer in whatever scheme makes sense to you. Reorganize it whenever you want, as often as you want, and as easily as you want to make it.
2) Get in the habit of backing up that computer "library" often.
3) OPTIONAL. Put that library on Dropbox if you think you may have an "I don't have anything to read!" crisis while away from your computer.
4) Put only a handful of the books from your permanent library on the Kindle at any given time (think of it as a book bag).
5) Delete them from the Kindle when you're done with them.
Works for me!
