I did my 2004. I put in a JL 500/1 amp and a JL 10" sub in a small box in the trunk. The amp takes the high-level speaker-outputs from the built-in factory sub for audio. You can either run an ignition-on 12volt wire into the remote-input, or have it sense a signal on the speaker wires, which is what I do. There's a microphone above the rearview mirror (behind the headliner) that you MUST remove, or you'll have many many many problems - huge volume fluctuations, etc. Most car stereo places, who dont know about the microphone, will refuse to work on it - which is what The Good Guys initially said. After he finished wiring up the amp, it sounded horrible, then i showed him how to remove the microphone by doing it myself, and voila.. Not only did he learn how to successfully install a sub into a Bose system, but my stereo sounded awesome. The install was like 80 bucks, 20 bucks for the wiring kit. The amp was something like 250, and the sub was around the same.. total.. about 600 bucks? You can find cheaper subs and amps, I'm sure.
Look up one of my old posts about the Bose system, and you'll see how to disconnect that microphone. You don't need it. Oh, here it is:
https://mbworld.org/forums/c-class-w203/35129-amp-sub-installation-problem-bose-audio-pilot.html