Is your factory system the base or the upgraded Bose with the sub built into the spare tire? If it is the base, you can do whatever you'd like with no problems (no need to bypass factory amps and crossovers). IF you have the upgraded factory system (I think it's only on Type-S) you will have to start from scratch (remove head unit, factory sub, all speakers, and run your own speaker wire to all speakers..... in essence as if there is no radio in the car to begin with.) I'll give you more help when you post your factory stereo type.