OK, I have been installing for curcuit City for four years. The the stereo you got is a good choice, much better than the stock one. You have two options. The guy you talked to is partially right. You have to either bypass the amp with a $15 Metra plug sold at curcuit or most any other Car audio stores. It wires right up in back of the radio. This sometimes works, but is much more prone to blow your radio, because it will be using both amps. We never usually do this in amplified Stangs Contours etc. What we use, and what you should get is a Perepheril Ford AD A Head plug. It is specifically made for this setup. It lowers the signal from the new head unit to counteract the amount of the factory one. You will still be getting your full output of the new radio. I have had this plug in my tour with my Kenwood Excelon radio for years now. Sounds great and I've never had any problems. The plug is $45 and you can get it at Curcuit. Its a little more but its worth it to do it right. It just wires up behind the radio simple and easy. Try That. Hope that helps.
p.s. I will admit, some people at some Curcuit Cities are out to screw you to make a buck, but don't worry I'm one of the good guys he he...