My experience had the players run two sets of PC's. We called them the "bridge crew", and the "away team". This allowed us to plan each get together with a task one of the two crews needed to accomplish, and sometimes in multiple occasions per session. In ours we called the main ship Orion, for who would be searching the heavens for the seven sisters but him? We called the scout (ISV-5) the "Sword', and the resource ship (LSV-5C) was the "Belt" of Orion, of course. The "Cedalion" was the encounter ship (Entdecker), just look it up.
For example, use the "bridge crew" characters to plan and roll skill checks for the warp to the next system for the fleet. The characters agreed earlier that the scout would always jump into system first, heading for the central star passive scanning the system. When no threat, send a message torpedo back to get the Orion. Warp the fleet together in new system, and then run a briefing on a potential surface mission, or anomaly discovery, dispatch the resource ship as needed (ice, gas, etc) switch to the "away team", which in my campaign was all the crew of the Cedalion.
My players wisely decided to not be any characters on the Sword (a player ran this captains character advancement, but we agreed he was an NPC while scouting), so that I could speed that part of the journey up by just delivering reports of whats ahead, based on my narrative/rolls when they rendezvous later. We also agreed the captain would remain an NPC, but I role played him like JL Pecard (always seeking council, acting on said council). We had 6 players; Bridge Crew was the Sword and Belt captains, the second officer of the Orion, Orion Pilot, Orion Doctor, Orion Computer Chief. They also played the "away team" role as the Cedalion bridge crew (not confusing at all), who were each Jack of all trades mercenaries, who could handle rough encounters and complications in the field.
Later the doctor character also played the chief astronomer scientist, getting a foot in the door on the stellar explorers part of the journey at destination for the players, as well as something else the doctor character could participate in, as Doc is often not needed. We allowed one alien PC, the Orion Pilot was a male Sung. We ran an additional cold sleep crew stash for specific skills needed, explosives expert, fighter pilot (they could 3d print one if needed), whatever. We could use it as a story element to replace lost field crew, hey Bill, roll up a guy, and we'll say he was in cold sleep the whole time...
Love the game since the 1989, mature role playing players and DM enjoyed roughly 1/3 "aggressive" flora/fauna encounters (aliens dies hard in us all),1/3 role playing the bridge telling the away team where to go and inter fleet interplay of personalities/agendas, and 1/3 the away team running the front line wet work required, including resource gathering and fleet logistics and maintenance.
Lastly, we enjoyed developing a quality of life index for the mission. I wanted to be able to reward experience for role playing, and have the same rewards as a tough physical encounter. Thus each type of adventure advanced your character, and were different, so everyone enjoyed. The QLI (Qualtiy of Life Index) was a score we set for fleet optimal performance (maintenance), life support stored and grown, culture/happiness of the crew. This was like an academic 4 point scale, and they tracked elements that became a mini game, with best crew rewards. Each point was a multiplier of experience awarded for the evenings play.
You'd laugh at the ideas they thought of, I mean a 5 year mission, hundreds of light years away from anyone! Make it epic!
