You will unless you hook the stock amp to the pre-outs somehow.
The only thing is, unless you can find the Scoche FD-15 bypass cable (I think that's the right part number) specifically made for the recent Contours, you'll have to do a little modification to the Metra one that everyone carries (5511 I think).
I wrote a little how-to on what I did with the metra kit, some extra wire, a little cutting and soldering and heat shrink tubing, in order to get the bypass to work right without cutting up the stock wiring. (I wanted to be able to put it back to factory.)
It's at:
http://contour.org/forums/Forum5/HTML/000865.html Hope that helps, it's a little confusing if you don't have the wiring harnesses right in front of you, but you'll get it if you see them and take out your factory amp.