are you keeping the original headunit? If so and the factory amp was in use, then the Headunit is most likely a dead head..meaning that no internal power. In any case, if you are using an aftermarket headunit, run the rca's back to the amp. Speaker leads go through the amplifier then to the speakers. ALWAYS rewire! Factory Ford wiring is not even close to sufficient for todays component sets. I have one single sub and it fires through the package tray in the rear. 3 amps, a 3-way set of components, one sub and Eclipse headunit. All I needed.
Let me know how things turn out. It is only right that with such a sweet looking car, you also clean up your audio signal too.