First off, you don't need any waypoints on the airfield. AI planes are coded to navigate the taxiways and runways and are going to ignore your waypoints anyways. Put your first waypoint where you want the plane to fly to after it takes off. As for the ammo refill, since nobody is going to see it rearm, just have it fly off for a while and rearm it with a trigger. Stick a gamelogic off in the corner of the map somewhere (give it a name), and when the mavericks are gone, order it to fly to the gamelogic with a trigger-
condition-
myplane ammo "MaverickLauncher" == 0 && (alive myplane)
on activation
myplane domove getpos mygamelogic
Now to rearm it, use another trigger-
condition-
myplane distance mygamelogic < 100 && (alive myplane)
on activation-
myplane addmagazine "MaverickLauncher"
Once the plane reaches the gamelogic, it will return to it's waypoints without any additional commands, and it'll be rearmed. Make both triggers 0 x 0 radius and make them both repeating. This is a very easy way to accomplish the task, although there are others...Or you could use the support pack like conrholio said.