Hey guys... It is actually very easy to hook up an amp and subs to your Bose system. You will need (obviously) the amp, subs, wires, an RCA adapter, and things called "Wire taps." There are other ways of splicing into the Stock bose wires, but I find that this is the easiest and cleanest.
Basically, the way I installed mine is: Ran the Power cable through my fender and to the back as Boominstereo suggested earlier in this thread. I grounded the amp to a bolt underneath my back seat. For the remote lead, I wired it into my fuse box. Now, this part was actually pretty easy. I used my wire taps to gain my High level output by tapping into the rear 6 x 9's wires (the positive wire is the one with the blue mark (you can see the blue mark on the clip on the actual 6x9), the negative is the one without.) These wires were then attached to my RCA adapter, which I picked up for $20 at radio shack. Then you just plug your RCA wires into the RCA adapter, and there you go. You now have your system wired!!!!! I will try to post some pics in a few minutes. (You can see the rca adapter in some of the pictures I already posted, and the red "wire taps" attached to my rear 6 x 9 wires) Any questions, please post a reply. I hope I have helped.
Whatever you do, do not let any audio installation shop screw you into ripping out your Bose stereo. There is not one part of the Bose that I had to remove!!!!!!!
Matrix.... I chose to splice into the wires after the amp (as you can see in my pics below). Other than that, I am sorry. I do not know which wires to splice into B-4 the amp

I hope what I have written helps you out though. Good luck.
P.S. From what I have heard from other people on this forum is that the Bose 6x9's are crossed over at 80hz, and I believe this is done inside the amp. This way, if you only want bass coming out of the subs, you can save money on a crossover by tapping into the wires AFTER the amp.
