Hmmm... Well, your first partition MUST be less than 2 GB to be able to boot from it using FFS, but once OS 3.9 is installed and both the boingbags (or at least the relevant sections) have been installed too, the rest of the drive should have no problem with FFS and SFS. I have a 40GB and an 80GB drive in mine with 15 and 20GB partitions on them, no problems...
