The factory sub won't really react much different with any sort of control, you really need to replace it. If i recall, when i took the sub out to look at it, it was very shallow mount (2ish inches) and a 1.7 ohm DVC...almost impossible to replace. You are better off either a) mounting an amp under the seat and building a custom sub enclosure in the existing place or b) amp in the sub location and a sub somewhere else (maybe just a box sitting in the back.