Also, you might need the newest version of SetPatch. My 19Gb HD only sees the first 2 partitions (below the 4Gb) if SetPatch from OS3.9 isn't running.
I use SFS for most of my drives, but I have WorkBench and 2 other partitions still on FFS (both above and below the 4Gb limit) and everything works ok as long as I have setpatch running.
SFS is on Aminet - make sure you get all the extra files aswell!
I don't know if SetPatch is freely avaliable though.