Help~ 02 Q45 Bose system

[Foler]

I just finished putting 2x 12W6's into my 2002 Infiniti Q45. Problem is it always sounds out of phase and crappy! I have my RCA converter hooked up to where the stock sub wires (took stock sub out). I had no idea what the problem was until I was informed that Bose's internal circuitry rolls off at a certain frequencies and you actually get no more bass when you turn the system up. Is there any way to fix this?

[PoorManQ45]

JL Cleansweep will remove the equalization from the OEM system.

Other then that the only thing to do is remove the stock system