One of the buttons at the bottom of the screen is the crew skill options, its on the far right. If the skill is passive, its a round icon. If its a limited skill, its a square icon. You press the square button and the skill activated, and you see a little timer on the square that shows you the time remaining in use, and then the time needed to recharge the skill. For instance, torpedo expert for reduced reload time. Its active for like 10 minutes, then goes grey for another 50 minutes or so as it charges up again.
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