Do bear in mind that the entirety of that first 'tutorial' mission has about half the features disabled. Not quite sure what you mean when you say you wandered around the pen and then left the campaign for it to say mission failed... I'm guessing you didn't sink all four ships/fire all four torpedoes. You fire the first shot, I think, and then you have to hit more ships/launch all four front torps before the mission will complete. It'll flash a yellow icon (and maybe a text bar) when you do. Then, and only then - head back to Kiel.
Once you return to the pen the first time (get back to Kiel and click the dock icon, then 'end patrol' like you did), you should get another little scripted section where the current captain is transferred and you're given official command of the uboat. Once this is over, the bunker will revert to the standard layout you'll be using for the whole rest of the campaign. Save & reload there.
You can talk to one chap for your torpedo and equip loadout (this won't work until you've saved & reloaded at least once), and another to open the mission select screen. Once the briefing has played, you can click on the map icons (or the list in the top left) to highlight and request a mission - then use the x in the top right to exit the map, talk to him again and select 'start patrol'. You'll get a loading screen (if you don't, you didn't save & reload, naughty
), then you'll be in the boat in the pen, with all the proper features enabled and all set to go. Only then does the game become a proper sim.
