Capn Charlie
Explorer
The ship, very vaguely, is like a character with ability scores (hence each system getting a system bonus). The crew provides the proficiency.So something about current ship combat, I'm assuming a weapons check that's described would be say computer use + proficiency or +/- the crew modifier from the ship, as would the counter roll be navigation + proficiency or +/- the crew modifier from the ship?
Crew quality is for when NPCs are doing stuff, when a pc is doing stuff use their proficiency bonus if they are proficient, plus the system bonus.
A normal attack would be resolved as ship weapons system bonus plus user proficiency opposing target engines bonus plus pilot proficiency.
Note that each ship module requires a user and an action. This means that if a ship has 4 different weapons (say, a pair of heavy laser batteries and a pair of missile racks) it requires 4 characters to fire them In a single round. If it also has dedicated comp stations to grant some weapons advantage, you need someone to man those as well. And someone with space vehicle proficiency to be flying the ship.
In theory this means that PC's with their good proficiency bonuses can only be so many places at once (twice as many for savvy engineers) and npc crew will round out the rest at varying costs to hire them. This means that particularly competent npc crew members acquired at lower salaries through narrative means (story awards) are ti be prized by players.