You have to use an option on mp3tofid to tell it to balance the fids across non size matched discs. I've got a 30gb and 20gb and use the following command :-

mp3tofid -Iis2 33 /data/mp3 /data/empeg/christa

The 33 is the part of the split. Although it looks wrong, my player is pretty balanced.

-2: percentage of files on second drive
-s: spread playlists over both drives