Starfighters would be used in ship to ship combat(maybe you could hit NPCs to be pilots while you control the main ship?) and there would be other types of ships as well, such as boarding craft. Drilling boats could be used to mine in a low gravity planet/moon or asteroid field. A shuttle could be used to get to a planet, and perhaps from a planet to it's moons or the other way around. When in the hangar, you would launch in a spacecraft by accessing the hangar interface, which would be somewhere in the room, and select the ship you would like to launch. This room would store shuttles, starfighters, drilling boats, etc., and to get spacecraft to put in the hangars, you would have to craft or buy them. Once you upgrade the ship to build a hangar, a large room would be added to the top or bottom of it. These mini-ships would be race specific and each type(shuttle, fighter, etc.) would have different variants or types, or upgraded versions. Well, that's about all, so I hope you like the ideas!
You can get modules on quests or chests (NPC villages can have lots), but its usually easier to get them in fossils (in the bonus chests that show up in the minigame) 3. When in the hangar, you would launch in a spacecraft by accessing the hangar interface, which would be somewhere in the room, and select the ship you would like to launch. Keep in mind that you need either the extra crew OR the phony license, but you NEED all the upgrade modules, or Pete wont have the quest sign to upgrade your ship.