ok so you have a wiring harness that came with the head unit and the stock wire harness that was plugged into the stock head unit. If those two match...then you're lucky! If they don't...(not sure if many do in the first place) you need to buy an aftermarket wiring harness that plugs on to the stock wire harness, and has wires hanging out the other end. You will have to strip the ends of the wires from the aftermarket harness you bought, as well as the ends of the wires that are on the harness that came with your aftermarket head unit...and connect them together.
If you have a GTS with the 8-speaker system:
Your wiring harness that you buy aftermarket will come with an amp interface so you can use the stock factory amp. This will come with simple instructions so that you wire the aftermarket harness from the car into the interface, and then you wire the harness from your aftermarket unit into the other side of the interface...and u're ready to go. I installed an alpine head unit into my GTS...if you have any questions PM me