Stevo'99

My wife's '03 Boxster S has the CDR-23 MOST fiber optic bus Bose stereo system in it and I am planning on replacing it. Is there anything I need to know about how to connect a new head unit, amp, etc. in the car due to this "revolutionary" system they put in P-cars in '03? I just finished replacing my entire stereo system in my '99 Carrera and now she wants to replace her crappy Bose system (which to her wasn't crap until she heard my new system).

I am planning on an Alpine head unit with ipod adapter and amps in the front trunk. I will replace the speakers in their stock location. I do need some help with what to do with the lame Bose subwoofer behind the seats. Has anyone recently tackled this and found a great way to upgade it? I was thinking of maybe trying to fit a bazooka in the space or something similar.

Any help, hints or things to avoid would be greatly appreciated. Thanks.