The submarine surprise strike shot happens before the general combat. THAT is their shot and they don’t shoot during the general combat portion. Assuming there are no destroyers present on either side, Here is how it goes after the combat move:
1. Attacking subs get a surprise strike shot at 2 or less. Defending casualties are moved behind the casualty strip.
2. Defending subs get a surprise strike shot a 1. Attacking casualties are removed immediately and the defender removes any units behind the casualty strip.
NOTE: Any capital ships that only took 1 hit remain on the battle board.
3. Any other attacking warships (NOT SUBS) and planes now fire. Defending casualties are moved behind the casualty strip. This can include defending submarines
4. Any other defending warships (NOT SUBS) and planes, including those behind the casualty strip, now fire. Attacking casualties are removed immediately and can also include attacking submarines.
NOTE: With no destroyers present, aircraft hits can NOT be taken on submarines.
5. If both sides still have units and attacker does not withdraw, repeat steps 1-4.
In any round of combat, when a submarine, attacking or defending, would normally roll, they may choose to submerge instead. Remove them from the battle board and place them back on the map.
So you see, submarines do not get two shots in a battle. The “surprise strike” is the submarine’s shot and they don’t fire in the general combat portion unless there is an enemy destroyer present, in which case subs don’t get the “surprise strike”. I hope this clears it up for you.