Hogan's Alley is where you put the Bridge Watch when you're submerged. If you leave them in place on the Bridge, and you take damage to the Bridge from depth charges, your crewmen will be injured/killed. It's all explained in the RFB readme manual.
As for the repair crew, man the repair crew slots with the most efficient men for the job. In the "Repair Team Priority" box, click and drag whichever box (damaged area) you feel needs attention first, to the top of the list. It works for me.
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