You don't need to put your music in your iTunes Library folder. You can put it anywhere you want, as long as you disable iTunes' "keep music folder organized" and "copy files to iTunes Music folder when adding to library" options (in iTunes > Preferences > Advanced).
So you can spread your collection over as many disks and folders as you want, organized any way you want.
Edit: If you're hellbent on letting iTunes keep using its automatic organization, you could rig it up by using symbolic links or aliases in your iTunes Music folder that point to folders on other disks. I forget whether you need to use symbolic links or aliases for this to work, but I know that it can work, because I've done it before.