To answer your question, the SCSI bus in a PowerMac 6100 will work with drives up to 2 terabytes. You can get a 2 terabyte SATA drive, connect it to a SATA-IDE adapter, then to your IDE-SCSI adapter and see the entire drive. I have a similar setup in my Amiga 4000.
With regards to how you'd format it, you could use FWB or other programs, but later versions of Drive Setup should be able to be used regardless of the make of the drive. However, I'd recommend 8.1 or higher (you can run up to 9.1, at least) so you can use HFS+ partitions.