From the perspective of a small ship, specifically a submarine, there are not enough officers on board not to utilize junior officers, particularly at battle stations.
Having said that, the junior officers are more likely to stand watch in engineering.
Officers are department or division heads as administrative duties. Their watches are in the command structure, which means that everyone on the bridge except for the officer of the deck is usually an enlisted person. Under normal conditions, you will always have one line officer (to use my previous terminology, one in the command structure) on watch on the deck (the OOD, Officer of the Deck) and one in engineering (EOOW, Engineering Officer of the Watch).
Even in battle stations, your enlisted operators will be the ones operating equipment. The Communications Officer does not automatically assume a radio operator position, nor does the Sonar Officer man a console and set of headphones nor does the Weapons Officer man the fire control panel.
Under most conditions, the captain of a submarine is a Commander (O-5) in rank and the Executive Officer is a Lieutenant Commander (O-4). During an advancement cycle, the captain may have been advanced to Captain (O-6) and the Executive Officer to Commander (O-5), but this situation will not last long.
Feel free to ask specific questions on submarine operation. I have no experience with surface warship operation.
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