Ideally I think the best way to organize your stuff would be to have it in the exact same way that it would be placed on your server. Then if ever anything should go wrong you could simply just connect your FTP and hit upload.
Unfortunately I don't have that system myself
I have a directory for every domain I have. In there I have the files places like they are on the server as well.
But all my free sites are in a directory called free sites with lots of subdirs for each free site. I then have an Excel spreadsheet with informations about there free site 1 is actually located and what picture set is used and so on. It works... but if I ever was about to move to another host it would be a nightmare.