Hi feelinlucky. I was a bit confused at first when I did my first patrol as well. I too finished the 24 hr stint and then twiddled my thumbs wondering what was next. I did eventually receive a message saying "continue hunting at my discretion" (or something similar). So I wandered off to find some action (I did, it sunk me
).
As far as I can work out, you can stay out for as long as you want (fuel and torps permitting). Messages coming in from bdu are sent out to all uboats (remember its a radio message, not recipient specific like an email) so you only need to take notice of the ones which apply to your uboat number. If I've got this wrong someone will shout.
As Sailor Steve says, when you do get back to base hit escape and go from there. I'm not sure how far out you can be before you get this option though. I'm sure some of the vets can let us know.
Hope this helps a bit. Have fun, good hunting.