I have a 2001 SE without a separate amp. I am installing a Bose head unit and will add my own separate amps. I don't have direct experience with the system you have but I have done some research so as to understand the quirks of the system.
Bonnevilles are not wired like any of the other cars you have experience with. They also use the radio to generate the warning chimes such as the ding-ding you hear when you have the door open etc. If you want to retain these, you can buy an adapter module. Also, you may not have the OnStar work with the new set up.
I believe the Monsoon amp will work fine for you (I think I have read posts where others have done this).
My first guess is that you need to have a signal to tell the Monsoon amp to turn itself on. Some head units have an output for this or it can be done with the same output that will extend a power antenna (although it may not be on when the CD is playing and in that case you will probably want to use a wire that is switched with the ignition key). This lead needs to be connected to pin A3 of the Scoche connector (if you use a wire from the ignition key circuit, you can do it back at the amp itself). It is possible that the connector does not have a contact in that slot. If so, I have one I can send you (it is a short wire with the contact that will snap into place).
Bonnevilles also have an AM/FM antenna system that uses a grid in the windshield and rear window (it looks like a part of the defroster grid). There is a module that amplifies the signal and that module will need to be enabled the same way the Monsoon amp is. The Scoche connector pin B3 will do this.
Good luck! I hope this helps.
There are others that are more knowledgeable (I learned this from them) and mybe they will chime in with more...
2001 Bonneville SE - Dark Bronzemist Metallic - Mods: 180* thermostat, iPod adapter, Digital OnStar Upgrade
Planned Audio System upgrades: Front & Rear 7 Band Equalizer, Amps, Hands Free Bluetooth Cell Phone kit
Planned mods: Front PEM, Ported LIM, Ported Heads, ZZP SR Rockers, Aluminum Gaskets & Reprogram PCM