I know I'm replying to a really OLD message here, but I just bought a replacement radio with GPS functionality myself, and was wondering the same thing.

What I found is that in my case, no ... I have to use the GPS antenna included with the stereo, rather than re-connecting the one from the factory radio. I don't think there's any functional difference between the two GPS antennas, really -- but the problem is with the non-standard connector on the end of the factory one. The Clarion stereo I have uses a GPS antenna with a square plastic snap-in connector surrounding the small metal connector on the end of the wire, and the round black plastic connector on the end of the factory one isn't going to snap in there properly. I believe there's a difference on the inside of the metal connector too. Looks like one has a small pin inside and the other has a socket for a pin.