Actually did this a few weeks ago - needed to set up a 4GB CF card for use in an A1200 instead of a regular harddrive. Partitioning went just fine in MorphOS, made two smaller FFS parts and one huge 3GB PFS3 part (remember to set max transfer: 0x1FE00 on the partitions if connecting to the internal IDE!).
One minor problem was the identical naming of these partitions, if I connect it now Workbench completely takes over :D but I won't be using this particular card as removable media in MorphOS..