before you start a mission, there is a screen in the "office" where you can select your upgrades to weapons, systems etc.
on the bottom left there will be a list of various u-boat types within your flotilla.
click the type you wish to upgrade to.
If the boat is not available for your flotilla it will not be displayed, you will have to use the phone to transfer to a flotilla which is host to the type of boat you wish to select.
hope this helps.
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