No worries, you're fine.
As you've identified you have 0 torpedoes left. I don't know why it reloaded one after you'd run out completely. It could be a bug or perhaps you made a mistake. The most practical way to replenish torpedoes and fuel, as in real life, is to
end the current patrol. Travel to your home port preferably, press the escape key and you should see an option to dock at the port. This will end the patrol. Alternatively I believe you can still do it whilst far out to sea - it will say 'end mission' I think. (Although in stock SH3 it might come up with 'abandon career' or something - don't click that).
From there all your torpedoes and fuel will automatically be refilled and several weeks will likely pass. You'll be in the game menus and can adjust your torpedo loadout if desired, make available upgrades, manage the crew and view your current stats. You can exit the game if desired and view your progress in Silent Hunter Commander. You're then ready to begin your next patrol and should receive a new destination to go to. Set sail again!
Your progress from the previous patrol is saved and your career continues. This is typically how it's done, as in real life.
As for resupply ships and U-boats I can't remember if they're found in the stock game, they would show on the map screen, but the large mods like GWX, NYGM, LSH, GWR, Onealex etc I believe should all have them. However they're a bit finicky to deal with sometimes and they only give you a partial resupply generally. They require the h.sie patch applied if you want the 'pseudo dock' option, which allows you to resupply from them without essentially quitting the patrol and starting another one.
Just try working with the first method and get into the swing of it all.
