Since waypoints are (unless disabled in the difficulty settings) always visible while in an aircraft, the easiest way is to have a waypoint that never finishes - for instance a Hold WP - and then just moving that one around as you see fit. The command for this is
setWaypointPosition. Simply move the waypoint when necessary from objective to vehicle.
Now, the problem with a moving vehicle of course is that you'd either need a loop to make sure it stays on the vehicle all the time, or then you need to attach the WP to the vehicle (like when you double-click on a unit and place a Destroy waypoint over it, that WP will remain on top of the vehicle even when you move it around the map, and the same is true in-game). The command for this in turn is
waypointAttachVehicle. I'm not entirely sure, but I would assume you can unattach it either by setting the waypoints position somewhere else, or by "attaching" it to ObjNull.
Those two commands should be enough to solve your dilemma
Wolfrug out.