[dnanian]

Glad that you're finding SuperDuper! useful, Rubber Ducky.

In general, when you're trying to synchronize two folders, it's best to use a program designed for "two way" sync. It's just too easy to make a mistake and accidentally overwrite data you may have updated on the "other side", even using finder.

What I'd suggest is using one of the two way apps like Synchronize Pro, Synk, or You Synchronize.You "could" use SuperDuper!, but I really think it'd be using it to do something it wasn't really designed to do, and thus the chance for error is much greater.