Many car stereos have a input that mutes the stereo when the phone rings (either a connected mobile phone car kit or a car phone), usually looks like a spare wiring hanging out of the back. Also some stereos have audio inputs available on the rear (in car nav / DVD etc).
It might be worth asking on some car forums about this, I'm sure there are some car stereo specific forums, but a lot of car club/type forums also have a car audio forum (the one I usually browse is Victoria WRX Club,
http://www2.wrx.com.au/forum/ , that has a good audio section, with a couple of professional installers answering questions, even if you don't own a WRX they'll be happy to help).