The conning tower is a place to put your watch deck crew while you are submerged and under depth charge attack. IIRC, RFB and OM use a similar damage model where everything outside the sub is much more fragile, but that will also include and crew that is supposed to be on the watch deck.
If you put them in the conning tower, they won't be as prone to dying when you are DC'd.
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OrangeYoshi
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