These positions are left open for you to make a choice, all I can tell you is what I know.
The gun positions, I fill them with permanent crew ( at Base), the conning tower and crew berthing are left empty for the following reason.
If you look at the watch crew stations you will notice that the empty positions can be filled by these crew members, so what I do in emergency dive is take the watch crews and fill the conning tower with the officers first and the rest of the watch goes into crew berthing this way these crew members are not injured as easily during crash dive or depth charging. After you will have to put them back to their watch posts.
The conning tower on a U-Boat is not crewed like a fleet boat. Fleet boats had sonar and radar stations in the tower, while U-Boats have the stations off the command room.
I hope this help's out.
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