Avoiding 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.
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.