@RYNO87
Submarines submerge during Step 2 of the General Combat Sequence only - if the player decides to do so. They are removed from the battle immediately, then.
This is totally independent of moving. This is totally independent of the Surprise Strike or other submarine’s characteristics.
Movement is affected by the “Treat Hostile Sea Zones as Friendly” ability: “A submarine can move through a sea zone that contains enemy units, either in combat or noncombat movement. However, if a submarine enters a sea zone containing an enemy destroyer, it must end its movement there. If it ends its combat move in a hostile sea zone, combat will occur.”
(Rulebook, page 27)
Again - this does not affect the Surprise Strike ability.