Crimson Garb
Need to get to work, so just a few quick notes.
Base off a Star Trek like ship bridge. Each user has a role.
Different ships have different engine configurations. Engines are large, small and warp. Large engines produce a lot of thrust in bursts (like chemical engines) but are inefficient. Small engines produce a small amount of thrust for long duration (like ions) and are very efficient. Warp engines allow short jumps. They're not actually very useful for getting where you want to go, but you can play cool tricks with gravity because you keep your momentum.
Combat
Choose what weapons to fire at what enemies and when. Also manages shields. Usual space ship stuff - shield can be surround or directional, and better for absorbing different types of attacks. Instead of hull damage, there will be a 'Primary Shield' that stops everything, but at the lowest efficiency. If there isn't enough power to deflect a blow, you lose. Different weapons are better for different enemies.
Science
Operates scanners. During battles, they can get more information about enemies. Often missions involve scanning some thing, or performing some experiment. Go scan some object, but our enemies are there too, so you'll be under constant attack. Being able to divert more resources to science means higher effiency.
Engineering
Manages power and systems. System can run above capacity, but it will overheat and need to run under capacity to cool. Any on-line system consumes power, taking a system off-line saves power, but that system will take time to power back on, it will consume power during it's boot phase and will be unavailable.
Communications
Interacts with other ships. Also can handle communication with beacons to get helpful information (dangerous areas, pirate weaknesses and so on).
Notes
This is one of those balancing odds games. Taking a safer route will be longer. Going a little out of your way to get to a comm beacon could give useful information. You can try bluffing an enemy.