I just got an '06 CS with bose too.
Try this link:
Bose Sound System - My Articles
You need to find a bag of poly pillow batting. I think my wife got it a Jo-Ann Fabric store. Or maybe a craft store. A bag of it is about five bucks.
Then, remove the center slat of the "vent port of your sub on the passenger's side of the floor. Pull up on the middle bottom part. It just snaps in and out.
Then follow the instructions. It's simple and it solves the Bose problem. It's a pretty nice sounding stereo after you do this.
Bose put a version of accoustic wave in a plastic box down there. The fix is that you stuff the box with the batting to kill the mucked up bass which kills the sound. The guy who came up with this is some sort of sound engineer. He even says to put a cap over the thing, but I think it sounds really good with just the batting. It takes 20 minutes once you have the tools (a ratchet, an extension and two small torx bits for them, and the batting.
Seems the Bose unit was designed for the Boxster with the top down or something. This fixes the problem. I like listening now. You can put bass and treble flat and turn on Surround and AudioPilot and crank it. Music is just MUCH better with tight, controlled bass that lets the other sounds come through clearly, for under $10.
-Six