Yeah, I never figured out companion skills properly either. Pretty sure the ones that boost your ship will work as long as they are assigned to your current ship's crew and your ship has the ship weapon type that matches their skill (for instance Barrett boosts ship particle beam weapons and Vasco boosts ship EM weapons), and I'm pretty sure the ones that boost one of the ground combat skills buff their own damage if they have that weapon type equipped (for instance you want to give Sarah a Laser weapon, Sam a ballistic rifle, and Andreja a particle weapon such as the Va'Ruun pistol). But I never did figure out how to use the outpost skills on companions, I can't even assign companions to my outpost even though I have hab structures and beds and such for them.
