You should use the Phase 5 HD tools, not the OS3.1 one, as it doesn't like the controller (or the >4Gig size or something, I forget). Anyway, use SCSIConfig and UnitControl I think the programs are. They're on the CSPPC disk(s) somewhere.
If you have a later version of HDToolbox you do indeed need to run it from a Shell as:
Shell> sys:system/HDToolbox cybppc.device
(assuming it's in Sys:System of course!)
