So here is the idea
There is a special editor place were you can make mini mission (or HUGE ONES)
in that editor it has a map of all of SP and you can place a way point at a starting position say Yeager airport numbered 1 the set the height of that way point if it is below sea level it just appears at 0ft
if it is below land level when the way point is placed over land it will just spawn on the surface of the land.
anyway way point one is placed at Yeager airport than number two could be placed at then end of the runway but a bit higher then number 1 then another off the edge of the runway and even higher then a series of way points all the way to wright and then land
For example you could plan:
Bombing runs
Airliner flights
Dogfight missions
etc.