Could you elaborate on that, please?
Sure. In terms of the different layers, I mean that, if you use a conventional "levelling" system for character advancement, then when you pick class features at level-up, you'll (almost) never be making a choice between choosing a starship-related skill or choosing a personal skill. Either there will be separate 'pools' of points to be put into each category, or some character levels will advance personal skills while others advance starship skills, or else class features will be designed to benefit both aspects of the game (so, for instance, the same class feature that makes it easier to spot enemies visually will also enhance your ability to use a starship's sensors).
The objective here is to avoid the "well, I built my character to be good at hand-to-hand [or diplomacy, or thievery, or psionics, etc.], so I'm useless at starship stuff" scenario. Whatever else you built your character for, you've also got the skills to help out aboard ship in a crisis - and if the players have been sensible, and their ship is reasonably versatile, they'll have a broad enough range of talents that everyone can do something useful without stepping on someone else's toes.
In terms of active roles, I mean that the characters who aren't manning the weapons or flight controls shouldn't be relegated to 'support' roles. To use a D&D party as an analogy, they shouldn't feel like the support-focused bard, doing nothing but improving other characters' rolls, or the band-aid cleric, fixing things when they go wrong (unless they enjoy those roles). Instead, the 'secondary' stations like co-pilot or sensors or comms should feel more like the primary spellcasters of the party, having access to an array of limited-use options that can really turn around a combat.
Someone manning the sensors could just be doing a 'target lock' to throw the gunners an attack bonus - or they could be performing scans of the wider battlefield, finding useful 'terrain' such as ionised gas clouds, spent torpedoes, or debris fields that can be employed to break up enemy formations or provide spectacular one-shot effects; or probing for weaknesses in opponents' defenses or sensors that open up options such as special evasive maneuvers or attack runs.
Likewise a comms officer could have their role expanded to include sophisticated electronic warfare, jamming, or management of drone fighters. And again, not done in terms of providing small, consistent bonuses - they should have a limited repertoire of much more powerful options that can be deployed at just the right moment, often in opposition to their counterparts on the enemy starship.
The key to making these secondary roles feel proactive and important is to get away from the "roll your check each round for a small mechanical bonus" mentality that a lot of systems have traditionally used. By giving them more powerful options, but making those options limited in how and when they can be used, even the occasional rounds when they literally are just reduced to 'support' tasks will feel less like dull routine and more like they're setting up for the opportune moment to unleash their full capabilities.