What's the best way to use SuperDuper to back up multiple hard drives to partitions on a single drive?

Actually this is quite possible to store the backups, all different drives on one volume with little effort. The magic words here are "back up to a disk image."

When you select the destination in SuperDuper one of the options is Disk Image. Just give the disk image a name and point it at your backup drive and all files will go into the disk image, completely accessible and completely separate from everything else on that drive.

If you like you can also encrypt the disk image for added security but you would have to create an encrypted sparseimage DMG from within Disk Utility first. I think that would work, never tried it but it makes sense it would.

drive is a partitioned HDD, is there anything I should be careful of when I format the backup drive

I think it is best to schedule at different times.The night should be long enough 😇. With rotating media saving to a dmg file, the arm will be moving all over the platter either at write time or at read time or even both. If you are using separate partitions, the arm is sure to be bouncing between partitions at write time. Thus, stressing out the arm.

I found my answer:

If more than one backup is scheduled for the same time, SuperDuper will automatically start them one after another until all have completed.

I assume that means SuperDuper will automatically start the next backup when the one that's running is completed, which is exactly what I want.

EDIT: Yep, that's what it means, and it works perfectly.