You can use up to 4 missiles/bombs at once. Launch more missiles than necessary to ensure the target gets destroyed in one pass, unless you are trying to get a higher accuracy bonus.
If you can see more than 1 target, you can shoot them down all at once using (pause)(pause)(pause).
The machine gun is very useful against ground targets. You can often destroy the target before the missiles get to lock on.
Often you don't need to shoot down everything to win.
Your grade can be SSS, SS, S, AAA, AA, A, B, C, D or E.
If possible, try use the advanced controls. They are much better when mastered, and allow you to avoid missiles much easier than the novice controls.