They used a sextant as the alternatives where even less accurate when there was no landmark in sight. The subs surfaced to use the sextant. That was some disadvantage especially after the allied forces became better hunting them.
That´s also featured in the movie "Das Boot". Two submarines met in a storm and the skippers come to the conclusion that they are nowhere near the coordinates they were supposed to be. The reason was a longer period of bad weather which did not allow to get a fix with the sextant.