Dual CF 4GB Cards. Which Filesystem to use?

[Oldsmobile_Mike]

You didn't say what size the two cards are.
 
Keep your Workbench partition under 500MB and placed within the first 2GB of formatted capacity, that should keep it friendly with any application that might not like large drives. Beyond that I usually ballpark around:
 
Workbench: 10% of whatever the capacity of your device is
Work: 20%
Documents: 20%
Games: 50%
 
And I'll throw in a vote for PFS, it was a PITA to set up but working fine now.

[Oldsmobile_Mike]

You could also use one as a primary and one as a backup?  Just copy the contents over from one to the other periodically?  That's what I sometimes do with my SCSI card readers, throw in a spare card and copy everything over.