If you haven't played Independence War recently, go through the original game's training missions to get acquainted with the ship's systems--the difficulty of the Defiance campaign ramps up immediately.
You can change your PBC (particle beam cannon) orientation mid-mission by going to the ARM screen.
In most missions, you'll want to save your missiles for later encounters. Stick to your PBCs until you're overwhelmed by superior numbers.
Some of the missions have branching paths. Restore to an earlier save point to explore the alternate path if you're having trouble finishing the mission, or if you want to try for a higher mission score.