Do I need two partitions on an external drive when backing up using Super Duper! and Crashplan?
Crashplan does not create bootable backups.  I'm not aware of the internal folder structure of the Crashplan backup, but the safest way to go is indeed to create an additional partition and perform a Mac OS install to it.  That way you're guaranteed that no folders will be overwritten etc.

If you use the FileVault encryption method (which Disk Utility uses), the disk will have all the same functionality that you would expect from an unencrypted disk once you have authenticated.  Just be sure to do so before your Crashplan backup starts or it won't see the disk.