you have to lose the external CDC if you want to interface w/ the factory head unit. I've installed ipods in both my Jetta and my allroad - its very easy, however the inferface adapter plugs into the CDC plug on the back of the head unit. People have made switches to switch between CDC and ipod, but theres a fair amount of work involved.
to be perfectly honest - i have a 6CDC built into my head unit in the allroad. Since i've had my ipod in the car i've put a CD in the player maybe one time. (assuming you've got all your CDs on your ipod)
