Just to clarify... factory NAV, aftermarket stereo head unit? If so, which head unit? Not all of them are designed to accept the interrupt signal from a NAV system, so they can shut off the music & play the NAV alerts. But I would think that if yours is compatible, it should have been part of the wiring harness connection. Plug & play, as it were.
It'll be interesting to see if there is a practical solution for you out there.