A couple other notes about FRED:
Karajorma has some great points in his FAQ about FRED. some good tips, mostly things that you normally don't even think of, like actually using the 3rd dimension of the environment you've been given.
Also, NEVER use Red Alert. It makes damage and weapons stats carry over from the previous mission, however at this point, it's incredibly buggy. Sometimes, missions with it just plain cause the game to crash. Others, ships warp in with ALL subsystems and turrets destroyed. Others, you wind up with a black screen and can't target anything.