It would probably be a very interesting balance. How much of engineering would you keep pressurized and at a comfortable temperature to allow easy crew access, and how much would you expose to space to save fuel/air/energy?
Again drawing from my own visualizations, those portions of engineering bays which store more important components and things that require frequent replacement would be pressurized with regular atmosphere allowing for quick easy access. Everything else would be either pressurized with non-recirculated inert gas (nitrogen or argon) for vacuum-sensitive components, or open to space. Large components would be stored in zero-g and accessed via a system of robotic arms or similar. Also, I see all exterior and within-armor-shell-but-still-in-vacuum maintenance being done by "Space Odyssey 2001" manned pods, similar unmanned systems, or robots running on tracks built into the ships.
Capacitor banks and power systems would be pressurized with nitrogen or argon and recirculated to remove ozone for increased component life. For some power systems, dedicated LN2 or ammonia cooling systems might be required (lasers and associated capacitor banks, large targeting computers, sensor arrays, battery banks), for others (less powerful computers mostly) the inert gas atmosphere would also be cooled.
Crew areas in exposed weaponry (turrets, missile launchers, etc.) would be normally depressurized, pressurized for crew entry, and sealed and depressurized during combat. The crew would wear full EVA suits with MMU's readily available and an escape hatch should the turret be irreparably damaged, but until evacuation was necessary they would be connected to life support ports integrated into the turret or similar.
On very large ships, especially those with long deployment times, the agroponics modules would be pressurized with an atmosphere specialized to the crops being grown, and serviced by an automated system. Crew would wear oxygen masks for entry and manual servicing and harvesting.
And yes, I overthink things. I should write a short story about a single battle in my envisioned spacecraft.