Each stat block for a vehicle has a "Crew" listing. It consists of the number of crew members in the vehicle, and a quality level. The "Crew Quality" sidebar (Star Wars Saga Edition, p. 174) lists the attack bonuses and check modifiers by crew quality. They are already factored into the stat blocks, but only apply when using generic crew. When using characters in combat, you recalculate for the character's statistics.
SWSE, p. 169 details how to handle "Characters in Vehicles". It breaks down the crew responsibilities into six main slots (Pilot, Copilot, Gunner, Commander, System Operator, Engineer) and two generic buckets (Other Crew and Passenger). The specific slots determine what the character can do, what skill tests they can make, etc. No more than one character can be assigned to each slot (except Gunner), but the same character can fill more than one slot at a time.
If you look at the statistics for the starfighters (starting on p. 178), you'll notice that many of them feature an astromech droid. This is a crew member with specific stats, and the stat blocks explicitly call out when to use this character's statistics, rather than the generic ones for the vehicle's crew.
So... When using a specific character to fill a role, you use that character's bonuses and attributes to make any required tests. It's a bit of a pain, but be sure to check test-by-test. For example, Attack Tests use the vehicle's Intelligence but the gunner's base attack bonus. The ship's Reflex Defense uses the vehicle's Dexterity with the pilot's heroic level or the ship's armor bonus.