hmmm...i used a lot choppers started flying.
try this:
create a empty chopper, make him start "flying", i'll use "chopper" as name for this example
create a pilot and in it's init field put:
this assignasdriver chopper; this moveindriver chopper
this should create a chopper flying at start.
the commands above work also for gunners (assignasgunner, moveingunner) as for cargo (assignascargo, moveincargo).
Not sure if a flyinheight command in the choppers init field would do something