Try to focus as much on fending off incoming missiles as shooting down planes as your final score is calculated by how many enemies you downed compared with how much damage you took.
Secondary Ship
Don't worry if your secondary ship is sunk during battle as it is only your main vessel that needs to survive each mission.
Status
During a mission an officer informs you of the status of your weapons and how much of the mission remains. Sometimes though this can be difficult to hear over the sound of battle.
Waves
Try to memorise enemy attack waves as there are some that go past harmlessly and then dive bomb you from the other side.
Weapons
Keep an eye on the prominent bars next to each weapon as these indicate whether they are ready to fire (white) or reload (red).