In STO, everything in the skill system stacks with at least two others. If you have not well understand, that you can read on, following we provide you an example.
The little numbers in the details equate a percentage bonus to a star trek credit. So to use Phasers as an example. Starship Energy Weapons gives you so much of a percentage boost to all energy weapons. Then if you go Beam Weapons or Cannon Weapons, that percentage boost stacks with Starship Energy Weapons respectively. Then, if you were to take Phasers it would stack with Beam Weapons and Energy Weapons. If you maxed 9 ranks in all 3 skills(sto credits), you would get 100% bonus when using Phaser Arrays.
The same works with all Skills, the higher tier skills provide more of a payoff in percentage bonus, but are more focused. The trick is finding what traces back to what. Look at the system something uses. In Science tier, high level(star trek credits) Emitter Powers will tie back to the Emitters Skill and the Operations Skill for example.