Well to clear things up, in my old car, I bypassed the amps like said above. I went to our local innovative audio, and was told if i used the above wiring harness then the signal that the actual 460 unit puts out is too weak of a signal.
The head unit sends very small signals to the amp that just tell the amp what to do, when using that wiring harness behind the head unit, it doesnt send a strong enough signal to aftermarket subs. The guy said my two 1200W 10's would only sound like 6x9's so this is probably your reason for no bass.
i used a small RCA adaptor that you tie in behind the amps. So in doing that, you wont run your RCA cables to your deck, they just plug to the adaptor, and the adaptor is tied or spliced behind your amps. so you'll have to keep the stock amp for the back speaker deck, and the RCA adapter gets a stronger signal from it. I spliced my adapter right behind the speakers on the rear speaker deck in your back window.
Like stated above its a pain in the ass. lots of panels and crap to move.