I don't know either...per se. I remember when digging through the Flotilla.upc files, there were the base names and then a set of coordinates.
Like, here's Pearl Harbor
Quote:
[Flotilla 1.Base 1]
ID= PearlHarbor
NameDisplayable= Pearl Harbor, Hawaii
ExternalBaseName=Pearl Harbor
AvailabilityInterval= NULL, NULL
DepartureDescription1= -18954703, 2562919, 45.918098 ; Enum of available points, choose one randomly each time a patrol is started
DepartureDescription2= -18954874, 2563059, 46.252201
DepartureDescriptionOut1= -18957616, 2548824, 242.189346 ; Enum of starting points for when the player selects the option to start outside the base
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The bolded section, I'm guessing, controls where your boat is when you start. I haven't tried anything to that regard but if you find the game coordinates for scapa flow and transplant them into an existing base you might get that to work. I'm not 100% sure on that.