I have a factory antenna. Ford drills your trunk for it. I put in an aftermarket head unit. Antennas are not compatible. My second antenna is hidden under the rear deck. You can't see it and it works fine.
I place the antenna just above the rear window (centered) and hid the wire between the window and the body of the car. You could also put at the edge of the trunk by the rear window, but I think they recommend it to be on the roof.
My GT had it factory installed on the trunk lid, but my Audio I just put it on the front dash in the center and ran the wire so it cannot be seen. I don't have any problems with signal surprisingly. Worth a try before drilling any new holes in your sheet metal.