Sorry to bring this back from the dead, but I just replaced the factory stereo and speakers in my 2001 non-Bose with factory amp. Not only is the factory amp a P.O.S., it has a built-in crossover that won't send any of the low end frequencies to the door speakers.
The Metra 70-2021 mentioned a few times will work to completely bypass the factory amp (behind the glove box) and send the speaker output from the new head unit directly to the front and rear door speakers, although you do have to swap the wires around (see below). Also, you'll lose the rear "subwoofer" (no big loss there) and the rear tweeters in the door pillars (also, no loss for me). At some point, I'll probably add a powered sub under the back seat but having the new door speakers with full range really sounds good enough for my back-and-forth-to-work-mobile.
To swap wire locations on the harness: Leave A1-A4 and B1-B4 in place and pull out A9-A12 and B9-B12. Then connect as follows:
A1-A9
A2-A10
A3-A11
A4-A12
B1-B9
B2-B10
B3-B11
B4-B12
To me, it was less f@cking around to buy the connector and swap the pins around than to run speaker wires to the amp location and cut/splice all the wires. YMMV.