Get in, shut the doors. Place key in ignition and the desired key fob in your other hand. cycle the key on and off(do not start it, just to were the wait to start is lit) After a few cycles of the key(5 if remember correctly, the door locks will start to lock and unlock as you cycle the key. While continuing to cycle the key, alternate depressing the lock and unlock buttons on the key fob. Press the buttons about 3 or 4 times and then stop. The key fob should work now. I think this procedure is in the owner's manual. Also, if you have more than one Ford, you can do this with both vehicles(both will work with the same fob) Hope this helps.
Scott