The factory NAV system has its GPS antenna installed inside the dashboard, just below the great big plastic piece that covers the top of the dash. The GPS signals easily penetrate the windshield and the plastic top of the dashboard.
It's been awhile since I've looked at the pictures in the service manual. I distinctly remember that the antenna is at the top of one of the "humps" in the dashboard. But I can't remember for certain whether it's directly on top of the instrument cluster or on top of the nav display. I think it's above the nav display, right in the center of the dash.