Did you know that you can heal helicopters? Just LAND (there is an option called land in the box on the right of the screen) them next to a repair unit and wait. While helicopters are on the ground, they are immune to ground to air fire, but prone to ground to ground weapons.

Anti-aircraft missiles are really annoying but you can avoid them by sending several planes at once. The thing is, when one plane comes, all units fire on it. When several planes come, enemy units will fire on all of them. And if one missile isn't enough to kill a plane, fire is spread out and usually won't kill any of the planes.

With some large civilian structures that have flat roofs, you can not only garrison units inside but move them to a rooftop loacation by using the move button on the roof. With V-44 heavy transports, you can even move and land tanks and artillary units on a roof!

P.S. Do not try to use Spinner bomb drones on rooftops as the drones will not be able to get off.

If you want to heal one of your guys but you don't want to take out of the building you can still heal him using the appropiate unit for the faction.
Eg. Send healing nanowave for Task Force Talon