I just got done installing the new JVC double din touchscreen dvd player and integrated the factory sub just fine. The wiring harness you need (at least from Metra for 03-and newer fords) is the 70-5521. It has the harness to plug in for the typical power, ground, illumination, and four speakers. It also has a second plug that connects to the vehicle's sub amp wiring on one side and has a remote turn on wire and an rca plug that you connect to your deck's subwoofer out.
Note that the amp remote turn on from most aftermarket decks (12v) is too strong for the ford factory amp (wants more like 4v). The result can be a loud thump or pop from the sub when the deck is powered up. This can be remedied by wiring in a 1500 Ohm (or 1.5 kOhm) resistor in line with the remote turn on.
Also, as has been said before, to be able to play dvd's without the parking brake engaged just hook up the parking brake wire to ground. Some decks will need a switch on this wire because they need to sense no ground first before they'll accept the ground. This is the manufacturer's way to thwart us from simply wiring it straight to ground and bypass their safety controls. Fortunately my JVC was not this way and I could hard wire it to ground.