Cartridge drives can either be given a mountlist, or have an RDB installed on them.
Since you are seeing the drive in HDToolbox, it should just be a simple matter of hitting the "Install" button to prep the disk.
Alternatively, see SYS:Storage/DOSDrivers. 3.9 comes with a file called ZIP and another called ZIC. ZIP is a mountlist for FFS Zip disks, ZIC is one for CrossDOS disks. Adjust the device/unit info to match. I think it's in the ToolTypes. It'll be whatever the device name of the PowerFlyer is, unit 2. IOTools in SYS:Tools might be useful, too.
EDIT:
If the PowerFlyer uses scsi.device, it's going to conflict with the scsi.device in the 1200's ROM. One or the other will probably be renamed to 2nd.scsi.device. Adding
SKIPROMMODULES scsi.device
to your Setpatch line in the startup-sequence might help. You also might want to download the IDEFix package - there's a tool in there called FindDevice which will give you a scan of everything on your IDE buses. Might give you a clear picture of how exactly everything's configured.
Also, have you installed BB2? There's a new version of the NSDPatch.cfg in it that may help with your missing partitions. It's not activated by default, so you'll have to rename Devs:NSDPatch.cfg-BB2 (or whatever it's called) to plain NSDPatch.cfg. Be sure to back up the old one, just in case.