Bird, I used this when I was running my subs off the stock h/u in my Titan.
NE7V TWO CHANNEL HIGH QUALITY LINE DRIVE ADAPTER - $19.95 : Zen Cart!, The Art of E-commerce
It's a line out convertor (LOC) that converts the stock speaker wires into white/red RCA inputs. That way the amp just plugs in. If you go to any quality audio shop, they'll be able to hook it up and allow it to control everything.
The only drawback to this is that it may still have the factory limitations, like no more bass after a certain volume level or whatever.
Now something like this is perfect because it still allows you to use your factory setup, and be able to adjust everything. The only thing is that it is more expensive.
re-Q - Take control of your factory stereo!