I suggest keeping the factory head unit and replacing the factory amp with your amp and subs. This will keep the RAP, chimes etc. and you will still have an unblemished dash. You may want to replace the speakers though, because the speakers for the Bose system are 2 ohms, I believe.
The biggest problem with factory systems is the power output and the speakers. Because the Bose system is "characterized" to the car, you may also want to add some equalization to be able to "tune" the response curve to the car, amp, and speakers.
This is essentially what I am doing. Since I have an SE, it didn't come with the Bose system and subsequently didn't have a separate amp. I have purchased a Bose system head unit and am in the process of getting everything together to do what I said above.
Oh, BTW, WELCOME!!!
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