[dnanian]

You have two basic choices:

- Reinstall El Capitan from Apple (using Network Recovery, I assume, if you have to completely wipe the drive). Then, when it asks you if you want to restore during the first boot, point at the SuperDuper backup.

- Boot from the SuperDuper drive. Properly erase and partition the drive. Then use SuperDuper's "Restore - all files" to restore.