Yes you can repartition your hard drive into multiple volumes, each of smaller size. But I think it's easier to tell your backup program to send directories A-M to external 1 and N-Z to external 2. I don't know if super duper can do this (it's billed as a whole drive cloning program) but other backup programs can do this no problem.
However, I would probably just buy a larger hard drive and relegate your older 3TB drives to secondary or tertiary backup.