I recently got a Garmin GPS unit and want to use
an external Gilsson antenna. It is a small square
magnetic antenna and I'm supposed to mount it on
the roof and then thread the cable into the inside
of the car.

Has somebody done this before who can give me
pointers? Thank you!

I have a Kenwood Navi unit with a small square magnetic antenna on a small metal square. I mounted inside on the center of the dash by the winshield. Works great.

Check the stereo and communications forum for many mounting ideas.