I was a little miffed at the explanation of this too.
How I figured it out is the following
1) Once you apply the upgraded item, look at your power out puts and see what changes. Mouse over your skills and see how much they are boosted. You can then figure out what skills are effected by what "stat/skill"
2) Look at your "skill list" and find the Lt. Commander Skills for deflector, emitter, sensors, shield etc- and read the examples of what powers the effect.
3) If the power you are looking for is not listed take a guess after reviewing like examples in step two and using some detective work from step 1.
I was really hoping that the powers would tell you what skill or stat they get their bonus from IE deflectors, sensors, AUX etc