I have a '99 Grand Prix GTP with a Bose sound system. I bought an Alpine deck(Model # IDA-X001) , a Sony Xplod 1000Watt 2/1 channel amp(Model # XM-2165GTX) , a 12" Sony Xplod 1200Watt sub with a box, Rockford Fosgate 4awg amp install kit w/a 100amp fuse, Install Edge adjustable line output converter(2-60Watts)(Model IEC AULOC) and i would like to install all of it in my car myself because they want to charge me $280 to have it done professionally at Best Buy because the Bose system makes it more difficult. I would like to know how to install these things and make it so it goes with the Bose sound system. PLEASE help me if you can!
In all honesty...if your vehicle has the Bose system installed in it and you planned on upgrading with the things you mentioned above it's not worth it. You'll ruin the clean sound that you more than likely have right now. Stick with the Bose setup. If you really want to change it... just wire everything separate from the way it's wired now. Run all new speaker wires and leave the stock amplifier that is in there now installed. If I were you I'd leave all the stock wiring in place so you can go back to the Bose setup when you decided to sell the car.
Oh and if you need that little bit of extra bass just install your line out converter and run that mono amplifier with your 12'' sub. Stick with the stock HU, especially if it has any special features such as steering wheel controls or heat/door chimes/alarm.