I would strongly suggest more than 2 partitions, especially if you want to have multiple versions of AmigaOS available. Booting into one system or another is possible, as said, but very difficult (you'll have to do a lot of tinkering with your 'default' startup-sequence that asks which system you want to boot into. It's much easier if you have multiple bootable partitions and select which one you want to use from the Early Startup menu.
Additionally, more than 2 partitions on the drive will make your life much easier if one of them fails. DH1 dies? No problem, back it up to DH2. That may not be possible if you set aside only a small amount of space for your SYS:. Or if 3.1 gets clobbered, you can run the salvage operation from 3.9's partition.
