Look at the UPC files in Data\Submarines\*class*Gato etc. Toward the bottom of the UPC file you can see the three watches - each beginning with the Aft Torpedo Room, then Engine Room, and so on.
Re-ordering these may work. If it gets into re-numbering all of the compartments this idea might fail.... Anyway, you can see how the Crew Berthing was added and where it shows up on the in-game graphic. Your idea may be doable - think positive, right?
Good luck & Happy Hunting!
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" Bless those who serve beneath the deep,
Through lonely hours their vigil keep.
May peace their mission ever be,
Protect each one we ask of thee.
Bless those at home who wait and pray,
For their return by night and day."
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