It depends on your crew loadout (buffing everything is much easier with two buff engis, and it also depends on other ways you run the ship), but here's the way I do it
Pyra (two buff engis): buff and pre-buff engines, then hull, then balloon/pre-buff front guns
Junker (two buffs): one guy buffs/prebuffs turnings and balloon, then pre-buffs top guns, then buffs/pre-buffs hull. Other guy buffs main engine, pre-buffs bottom guns, buff/pre-buffs hull, buffs front gun
Galleon: buff/pre-buff engines, pre-buff bottom guns, buff/pre-buff hull, buff/pre-buff balloon.
Goldfish: buff/pre-buff engines, buff/pre-buff hull, pre-buff main gun, buff/pre-buff balloon
Squid (two buffs): buff/pre-buff engines, then balloon, pre-buff front and right guns, if there's nothing else to do buff/prebuff hull.
Mobula (two buffs): Haven't tried, but I suppose you'd want one handling each side, so both get two guns, hull/balloon, one turning engine, then move on to main engine (and front gun?) once done.
Spire (two buffs): one gets main engine, then balloon, then top left gun. Other pre-buffs main gun while loading ammo, then turnings, then hull.