Workbench or the OS should go on the first Partition. 250-500MB is heaps for a System partition.
Less than 4GB partitions are fine for OS 3.1.
On my A1200 and A4000 I have 8 GB drives with a 500MB System and 2 x 3.6GB Partitions.
OS 3.1 on the A1200 and 3.9 on the A4000.
(Man... Lando guzumped me by seconds)
Goodluck.
gertsy