OK, a quick update. I managed to partition the 80GB drive using the OS3.9 Emergency Boot Disk.
I had a OS3.1 system set up (with the Deneb, FastATA and Cybervision 643D) and my mistake was to try and partition the other large drive BEFORE installing OS3.9.
I made the EBD (Emergency Boot Disk), rebooted the system from that with the OS3.9 CD inserted and the EBD HardDriveToolbox managed to sort the drive out. It still didn't read the drive configuration correctly (It thought it was a 27GB drive), but once I entered the correct number of cylinders, heads and blocks per track it did the rest. On the partition screen it divided the drive up into several FFS partitions by default, but I quickly deleted them and made two equal partitions using SFS. A quick format and another reboot using the EBD and I installed OS3.9 from the CD to the fiest 40GB partition. OS3.9 also copied over my FastATA prefs and my Cybergraphx setting so it booted up into a nice 1024x768 display.
Now I can reformat the original hard drive with the 17 partitions and turn that into 2 more large partitions to back up the other drive.
Then it's reinstall Deneb and see if I can get my USB ethernet card to work. I tested it under the OS3.1 installation and the Deneb identified and mounted it so hopefully I'll be posting from AWeb shortly.
Wish me luck!