Most special officers work it they're in the right compartment. You can see the light change. However, many of them don't work unless you activate them. Should be a icon with a sailor in it, but it's the icon for special abilities. Click on that and you will see icons for each special officer you have. You have to click them on for their ability to work. Some only work for a time period, so use them when needed.
I think Sledge covered the rest. Not having a boat of officers is realistic anyway. You also want to be careful letting experience officers go. Many of them will gain special abilities after promotions, medals or just time on boat....That way you don't have to pay for it.
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