Disclaimer: I retain no responsibility for you burning up your car, frying electrical components or messing up your car. This is for informational purposes based on my personal experience wiring an aftermarket head unit into my Audi TT with a BOSE system
2001 Audi TT w/ Bose (should apply to all Bose systems if they all have this common ground feature)
Do a search for the Bose harness to get the wire assignments in the connector. I believe I used one from a FAQ in the S4 section of the tech articles
After a ton of research and not finding anything definite I decided to just dive right into the project and risk blowing up my new head unit Bose amplifier and god knows that else.
The problem with the Bose system is you only have one wire from the head unit running to each speaker and you have one common ground wire for the whole bunch. You CAN use the line out wires (the powered ones, not the RCA's) on your radio harness to run to those speakers. I read people saying that you can't because it messes with the Bose amps power and will blow it and the speakers take different OHM loads, etc. Granted it's not super clean sound but people that I asked said they couldn't hear the slight hiss in the background. Even with the volume only moderate and the sound of the motor in my TT you can't even detect the hiss unless the car is stopped and the volume is all the way down. By the way, the hiss stays the same volume whether the radio is at 0 or 25 volume level.
Wire the positive wires on the aftermarket harness to the car's speaker leads. (You will have to strip behind the factory harness and cut the wires you need to use and solder them to your aftermarket harness.)
For those of you not familiar with flux or heat shrink tubing I suggest you start now. When you dip the stripped wires in flux you can essentially suck the solder right to them. Slide a piece of heat shrink tube one on of the wires. Dip both ends of the wires in flux (it doesn't need to be gunked just coated on the wires.) Touch your solder to the end of your iron to give you a small melted bead on the tip. Hold the 2 wires side by side and touch the bead of solder to them. About a half second later the solder will be deep into both wires and have a strong bond. Slide the shrink tube over top of the solder job and feather a light flame over it to shrink the tube (don't burnt he car up doing this :) Rinse and repeat for all wire connections you need to make. Bad connections give you noise on the lines so take you time and do each wire like this that needs to be stripped and connected.
The Schosche adapter only useless the plug on the car that has the power ignition wires, etc. Take one of the negative (ground) wires on the aftermarket harness and solder it to the common ground on the car connector. (One of the wires you cut on the back of the car connector) I haven't tried to ground the rest of the negative wires on the harness to the car I just taped them up for now, but the point is I DO get sound from the speakers which are connected to a Bose amp.
I am anal about my sound so I will hook up an external amp pretty soon here but I wanted to tell people that it is for sure possible to get it to work. You don't have to wire all new stuff in the car in order to get music playing from your new head unit and existing Bose system. Ground loop isolators for speaker level noise filters can probably be used to eliminate the hiss so if anyone has tried this feel free to update this FAQ
Another option which I haven't tried but read some tidbits about is to plug in RCA's to the line out jacks on the back of your new stereo and cut the other end of the RCA cables. You should then be able to wire the positive wire to the car wires and connect one of the shield wires (essentially the negative on an RCA out) to that common ground on the car. This might eliminate the hiss since the power is only coming through the line from the Bose amplifier to the speakers.