Depending on which nav you installed, but when we install an aftermarket(Pioneer,Eclipse etc...) we put the antenna on the dash up in the far corner nearest the pass windshield. We have never had any issues but keep in mind on the ones we install you must connect speedsense wire which helps tracking also.
If it is the factory nav system, the ant is on a cross piece in the dash. When the system is installed after the fact, the placing seems to be anywhere under the dash with the up side up! I've been told it sits well on top of the ducting!