The Ford premium amp is located behind the glove compartmnet. You can access it by squeezing the glove compartment sides inward to release the stop tabs - the compartment should then drop all the way down to the floor. The amp is that little 90 pound weakling with the fins. It puts out about 10 watts RMS per channel...with a tail wind...on a good day...when all the planets are in alignment.
I don't know about the factory CD deck, but my original cassette deck did not have RCA outputs. The Blaupunkt that replaced it sounded much better (I bypassed the factory amp) even with the stock speakers. I currently have 3-way 6x9's in my doors and a 200 watt power amp in the trunk. I don't listen to Rap or Hiphop, so the 6x9's are perfectly fine for me. A Nakamichi CD-40z CD deck will be replacing the Blaupunkt soon.

Good luck with whatever you decide upon for your sound system.

-Wes
98 SE Sport