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.