[Treetop64]

The answer to that question is specifically explained in detail in the pdf manual that comes with RFB. There is a lot of other good information contained in the document that covers all the other aspects of the mod, so reading it is highly recommended.

In short, if the crew is left on their lookout watch stations when the boat dives, the game "thinks" they are still at those stations. So, if you sustain a depth charge attack and take damage, those crew members left at their lookout stations are that much more susceptible to becoming casualties. Therefore it is recommended they be manually transferred to both inside the conning tower and Hogan's Alley/DC team, as described in the manual. This is a limitation of the game engine - moving crew members around when diving wasn't implemented simply to give the player something to do.

As for the vacant helm and dive stations, I simply transfer in new seamen to permanently man those stations before I set out on the first patrol. When diving, I transfer the lookout watchstanders to Hogan's Alley and DC parties, since the dive station and helm is already manned.

As a note, you don't have to manually transfer crew every time you dive, only when you think there is an imminent threat of depth charge attack. You have to use your own judgement.