OK, I didn't realize you had a separate sub, I thought you were just replacing the 6x9s in an otherwise stock system. In the factory system, the 6x9s only get very low bass signal, your midbass has to come from the door speakers. The only reason to keep the 6x9s is if you want to conserve trunk space, since you already have a sub in the trunk just get rid of them. If the midbass is weak you need to add power to the door speakers to match the output you are getting from the sub.