Well when I had my Infinity's hooked up to the Bose Amp, I used the OE wiring. I just bought aftermarket adapters from Best Buy to hook into the Pontiac/Bose connections that then plugged into the Infinity speakers in the rear deck. As for a subwoofer, I am not sure how you are going to complish that little feat. There are no connections for a subbox on the HU or Bose Amp. I am sure there is a way to hook it.
I know one guy in KC who did it, Curtis here on the boards is the person who did. I will try and find out from him.
Sorry I cant be more help than that right now.