I just installed an aftermarket head unit (HU) and new speakers recently in my '09 CC. I personally chose to route my own wires between components, but you can still use the factory wiring harness to hook up the factory speakers to the new HU.
Download the manuals and look up the Audio section for the wiring guide. All you have to do is splice the harness's wires into the HU's wires, and you're good to go.
I live in Quantico and can help you install it, although finding convenient times will be a hassle with my work schedule this month. Also, don't forget to purchase a Factory System Adapter! I got mine from Crutchfield > Car Stereo Installation.