Thought of something that might be useful here.
Basics of ship combat and the stuff you can do therein.
So ship combat takes place during what are called Strategic Turns, these are significantly longer than the usual 6-10 seconds of a normal combat round. This is because realistically speaking, ship combat would be fairly slow and ponderous, the massive ships maneuvering into positions to place the enemy within a firing solution while stay out of theirs. Since they are longer, more usually happens, for instance, instead of each ship doing something per round, each PC on board the ship may take an action.
Examples of shipboard actions
An Explorator might roll a Tech-Use to overcharge the engines without damaging them to give the thrusters a one-time boost in order to pull the ship out of the enemies targeting range while keeping them in position for your own attacks. Or run a focused Augury scan to gain information about what kind of systems the enemy ship possesses.
A Voidmaster might be at the helm and roll a Pilot (Space Craft) to Flank an enemy ship for a macrobattery barrage or a Hit and Run boarding maneuver. He might also be at the weapons station to roll the Ballistics test for shooting down an enemy ship.
A Master-At-Arms can perform the actual Hit and Run, commanding his troops as they cause havoc aboard an enemy vessel. Or alternatively repel an enemy boarding party.
A missionary can use his oratory skills, charm/deceive etc... to maintain crew morale under pressing conditions, oftentimes this action will be what keeps the crew from mutinying.
The Rogue Trader himself is the one who gives orders out, he decides who to target, where to move the ship, etc...
Keep in mind these are only examples, if you think of something mention it and if there is no listed skill test I may very well be able to think of something that would substitute effectively.