Best way to mount a GPS unit in a car is have the GPS base inside the car and the antenna basicly on the middle top of the roof. This position provides as little metal interference as possible. GPS's work best being as high as possible to avoid the signal coming from the top down from bouncing off the metal.
I had mine located in the middle just outside and above the front windscreen with the cable going along the top and into the door rubber trim. Works great with usually 12 visible sats showing up most times.
You need to make sure your antenna is waterproof as well, you can buy them (like mine) which are and also include a magnet at the bottom of the plastic case.
Makes them very easy to stick on to the top of the roof's. However you might like to secure them on with something else also as magnets tend to lose their power after a while.