right now, I am running OS3.9....so to be clear, I need to boot with 3.1 and begin the configuration?
No, you don't HAVE to.
What you could do is, set the SCSI ID of one drive to an unused number. Putting the Logical Unit Number to the same value should avoid conflicts with your existing drive.
Then, plug connect it to your existing setup, and see if HDToolbox will let you access the drive.
Probably not, because it is already formatted (being an older drive).
Technically SCSI supports hot plug, but not hot unplug (you can add a drive to a live system, but not remove it without crashing the system).
Or you can err on the safe side, and power off before connecting the drive.
Either your Amiga will not boot, or it will. After that, it's a question if HDToolbox can make sense of the existing partition information.
I understand there is a hard coded limit of 65K maximum surfaces, so it will almost definitely overshoot that.
BUT, if you don't take a shot, you can never hit.
One issue can be, with a 10K drive, you have to reboot anyway. Because the drive takes longer to spin up to working speed. Should not be a problem with the Cheetahs, they are quite new, in comparison to older 10K drives.
This is why there is some sense to spinning up the drive, then attaching it.