The monsoon amp is mounted on the left side behind the back seat:
If I remember correctly, the amp only has 4 speaker inputs which it splits into 8 speaker outputs. Two inputs for the front which is crossed over and sends high to tweeters and mid range to door drivers, and two for the rear which is crossed over and sends lows to rear 6x9s and mid range to the rear door drivers. If you plan to replace the headunit you can and should bypass the amp. There are two harnesses in the amp. One contains the wires coming from the radio, the other contains the wires to the speakers. I made a wiring diagram based on my car, might work for yours as well. Notice you can only hook up 4 speakers though, so you will want a component kit for the front doors so that you can use those two feeds to feed all four front speakers, then you choose either rear doors or rear 6x9s.
For the 2003 Bonneville with the Monsoon amp, there are two bigger harnesses going into the monsoon amp. One is an input from the radio, the other is an output to speakers. The speaker wires are in twisted pairs. I believe Brown is LeftRear +, Yellow is LeftRear -, Dark Blue is RightRear+ and Light Blue is RightRear -. Not sure about the rest but, if you are bypassing the amp, the wire on the left side of the diagram gets connected to the wire on the right side of the diagram. Atleast that is how it worked out in mine.
Eventually I gutted the car and ran all new wiring, but perhaps the above will be helpful in your endeavor or convince you to do the same as I did: