This is precisely what I have been working on all day.
A relatively small disk for the system and a large one for ibays and some selected home directories.
I have things more or less working now.
Moving ibays and using symlinks works great,although I had to change the Apache config a bit to let Apache follow SymLinks. For the home directories I have chose not to move the complet home directories, but just the "home" part under the user's home directory. In that way, all mail stuff etcetera is still on the system disk. But I don't know of any reason why you can't move them completely.