I also often leave the cockpit for a while and my "virtual FO" takes over from me. Now if that means that the GPS covers the gap for my pretending he is following the VOR to VOR route, then that's fine by me.

You need to remember that we all take the realism of FSX to whichever level we choose. So if we choose to use the GPS, real or not, we choose to use it. I choose to use it if I want to. ;)

The way it works is fairly simple. It follows the plan waypoint to waypoint. It does not care whether those waypoints are VOR, NDB Intersections, Fixes or just a spot where we create a user waypoint on the map. So it follows whatever plan we load into the sim.

Mark