Prepare your mission flight paths and gather all your information and reconnaissance as soon as you can. When the situation gets busy you can keep your attention on the enemy and not your own units.
To bomb a ground target yourself, send a reconnaissance aircraft to film it first. After that, view the target using the camera icon on the command screen. This will prevent accidental bombings of innocent civilian buildings.
Avoid sending 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 try to scurry away.