Just wondering if I got this right:
In the rules it states:
Opposed System Tests - During an Opposed System Test, both players will roll one die and add it to the matching System Rating. Each player can also play one Command Card to modify the test. pg 9
It is later stated that:
Crew Cards - When you play a Crew Card from your hand, you must assign it to a ship in play. The Crew Card grants a permanent bonus to that ship, as long as it remains assigned to it. pg 26
My assumption is that during combat the crew (Command) cards on a ship add a cumulative total permanent bonus for that ship - plus - you get to play one command card from your hand (or forfeit one of your crews ability to use their combat text).