I initially just plugged the antenna into the aftermarket stereo. I think I may have had to have a short extension or something. Since then , though, I did away with the factory antenna and installed a hidden powered antenna that is under the back tail piece. The stock antenna isn't worth much in performance and was always bent over whenever I had luggage on the luggage rack anyways.
I am getting ready to replace the aftermarket stereo with another aftermarket stereo. Color display and some other cool factors. Putting this in.
http://www.rockfordfosgate.com/products/details/pmx-1r
http://www.rockfordfosgate.com/products/details/pmx-8bb