In most combat, every ship in the attacking fleet fires, followed by every ship in the defending fleet - even those that were destroyed by the attacker. If there are survivors on both sides, round 2 is the same as round 1.
With SW, every ship in the attacking fleet fires, but the defending ships destroyed do NOT get to fire back. Note this is for the first round only, and only when the attacker is the civ with SW. If the defender has SW, it's the same as normal combat. If there are survivors of the first round of combat, all following rounds are like normal combat.