captain:
stay within 500 meters of your ally ship.
That alone will help a lot.
Engineer:
accept loadout of captain
if captain doesn't give a loadout then choose a standard kit (spanner, mallet, fire ext) and take the proper ammo for the gun you will use
Gunner:
take pipe wrench and proper ammo if captain doesn't give loadout.
section off the ship. Assign parts for people to repair. I will give the standard ones / ones I use:
pyramidion:
Engineer 1 - top left gun and balloon
engineer 2 - hull, turn engines and main engines
gunner - top right gun
Goldfish:
engineer 1 - main engine, balloon, turn engines
engineer 2 - hull, right gun, front gun, turn engines
gunner - front gun, left gun, hull
Junker:
Engineer 1 - balloon, turn engines, top left and top right guns
engineer 2 - front gun, hull
gunner - bottom left and bottom right guns, main engine
galleon:
engineer 1 - repair gunner's main gun, turn engines, fire other gun when not repairing and hull if ship has to tank damage
engineer 2 - hull, balloon, main engine top left gun
gunner - main gun (usually the front left), any other gun if necessary
spire:
engineer 1 - top left gun, balloon, turn engines, main gun
engineer 2 - top right gun, hull, main engine
gunner - main gun and bottom left gun
or
engineer 1 - top left gun, hull, main engine
engineer 2 - bottom left gun, balloon, turn engines
gunner - main gun
mobula:
engineer 1 - bottom left gun, hull, left turn engine
engineer 2 - bottom right gun, balloon, right turn engine
gunner - top left, top middle, top right guns, main engine
Squid:
engineer 1 - balloon, left side engines, hull, rear gun
engineer 2 - right side engines, right gun, buffs
gunner - front gun, hull