[dnanian]

I'm having some trouble following what you're asking here. But, if I understand you, SuperDuper! is only going to back up the volume you select. It won't back up other ones unless you choose those - and yes, they should be on their own partition: each source volume should have a corresponding destination volume (partition).

Help > Frequently Asked Questions, in SuperDuper!, has instructions for partitioning.

Hope that helps...