Setting waypoints:
Do not send missions over well-protected enemy positions. Instead, set the mission waypoints to skirt around them. Ground vehicles can be used as mission waypoints so your planes can home in directly on them as they attempt to scurry away.
Flight paths:
Prepare your mission flight paths and gather all your information and reconnaissance as soon as possible. When the situation gets busy you can keep your attention on the enemy and not your own units.
How to avoid anti-aircraft:
Keep your planes at as high an altitude as possible to avoid anti-aircraft fire.
How to avoid civilian casualties:
To bomb a ground target yourself, send a reconnaissance aircraft to film it first. Then, view the target using the camera icon on the command screen. This will prevent accidental bombings of innocent civilian buildings.
Combat air patrols:
Watch your combat air patrol planes. If they chase enemy aircraft, they can fly off over enemy territory and get shot down by SAMs.