You can jumper the RSA system relatively easy... 4 wires going in are the same color as the 4 wires coming out and they are all twisted so it makes it easy... I did this in my '03 because I thought the RSA was dead causing my rear channels to not work. (The rear channels from your deck go through the RSA before they reach the amplifier. The RSA uses those rear channels from the deck to provide the audio it makes available for head sets.)
There is a subwoofer in the console as well...
There are 4 channels coming from the radio to the amplifer and 6 coming out of it. From what I could tell it didn't look like the amplifier has any cross overs in it and GM expects the speakers to filter out what they can't do. (Except the tweeters which have a capacitor on them to block bass.)
If you are adding an aftermarket amplifier while doing this swap then you can do the amp bypass at the deck with an aftermarket harness and basically remove the console harness. I have NOT tried to remove the console harness but I have to believe a portion of it goes to the back of the deck and other portions go other places. You might be better served finding a donar non-bose system and grab the harnesses and such from them.
Another option might be to build your own seat and integrate the amplifier and subwoofer into them... Then it would be reasonably simple to run the wiring under the carpet. And depending on how an add on seat might fit you might be able to install the amplifier and subwoofer under the seat somehow.
I relocated mine under the passenger seat. It BARELY fit, required some removal of ductwork and was in conflict with the front seat. (I installed a PC where the amplifier normally sits.) I have since gone to an under seat speaker box (Which has not worked very well from day 1) and a sub amplifier (Temporarily mounted to the back of the seat.) This allowed me to take the BOSE subwoofer and remove it from the system. I then cut up the speaker housing and now house the BOSE amplifer inside the subwoofer housing. Works decently and leaves lots of room for expansion stuff when I get to them. I will be replacing all my amplifiers with some aftermarket ones which will allow me to completly get rid of the amplifer and subwoofer from BOSE but I am still tying into the harness under the console for now...
Ok, I went off on a tangent there but you can see it is not just a simple unbolting and replace.
Rodney