Match the colors of the wires from the aftermarket stereo to the colors of the wire harness. Your instruction manual for the deck should tell you what color does what, and if you buy the harness from best buy, it'll have instructions on which colors does what too. Crimp the colors together, making sure you have a solid connection. I like to wrap the crimp connectors in electrical tape to make sure there are no shorts, to make it more secure, and keep it looking cleaner.
Now, to make things more difficult, if you have a mach 460 audio system (I think you do, although I'm not sure if v6's have those), Ford put in 3 stock amps. One under the CD player, and two in the trunk. They are 5V amps. Your stereo deck will be putting out 12V. Because this is not balanced, every time you turn your car on the speakers will make a very loud pop. It gave me a headache. Do not skip this step, because you will become very tired of this pop and end up doing this anyway.
This is a very well made instructional video on how to tie two resistors together and ground out a lot of the voltage, making the pop so quiet it's almost nonexistent. You can pick up the two 1k ohm .25 watt resistors at Radio Shack for $1.50 a piece. Follow the video carefully and it'll be easy. https://www.youtube.com/watch?v=vFIe3IIJIds
2000 Mustang GT
My pride and joy, my first car ever. Bought on 6/2/2013.
Check it out at my channel here: youtube.com/mustangfanatic95
Expect more vids in the Spring: Car shows, cruises, fly-bys, etc.