It's unclear which Rockler jig you have. The current model appears to do through DTs, half-blind DTs (I think what you are referring to as offset and rabbet), and box joints. You may have an earlier model that doesn't do through DTs.
The type of joint depends on the template(s) being used. Half-blind and box joints use the same template - the one with the straight "fingers". Through DTs use both the straight-fingered template for the tails, and the angled fingers for the pins. Set-up specifics depend on the type of joint being made.