I've backed up and wiped several times now, going through the various builds -- make sure to back up! Let yourself start with a clean partition. Although it's not necessary, it greatly increases your chances of leading a normal life post-install.
Hmm...I don't think you need to partition both drives. If it's convenient to keep a 9.1 system on one and X on the other, that would make sense to me. Startup Disk, which switches between bootable volumes, will scan your SCSI and other ports, so it will find other physical drives as well.
Startup Disk will scan all drives that are compatible. That's important. I don't have 100% confidence in X's ability to recognize non-standard hardware...at least not yet. Best to check against the list of X-approved devices.
Well, we have OS 9.1 on our 30 gig drive and MacOS X PB on our 20 gig drive. apples new startup disk control panel (the one in 9.1) has no probllem switching and will even let you pick what system folder on the same disk to boot off.