I assume you are running Operation Monsun? If so, you can select your UBoat type during the career start process, same place you pick the career start date; it really depends on which Flotilla you join. For example, Flotilla 7 usually starts with a Type IX out of Wilhelmshaven. As for upgrades, they are offered when you are in port. Most will cost renown points earned during previous missions. Hope this is what you were looking for! Good Hunting.
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