You should stay on the surface. You lose huge amounts of range, speed, agility and situational awareness when you dive. You dive when you detect something that you don't want to be seen by, or if it's already seen you and you need to get away from it.
Later in the war when u-boats changed from being the hunters to being the hunted, it became harder and harder to stay on the surface and so innovations like the snorkel came into play in an attempt to let the u-boats stay submerged as long as possible. This culminated in the Type XXI boats which were the first submarines intended to operate entirely submerged, and were the template for all major navies' submarine designs after the war.
Also it will take a long time or sailing to get to your patrol grid, but you should resist the urge to shorten the journey by travelling at high speed. Large and medium size boats cruised at 6-7 kts, which you can manaully set yourself, or just choose 'ahread one third' which will make you run a bit faster than this but is a reasonable approximation. You can also experiment with asking your navigator to tell you how far you can sail at your current speed (this will change depending on the weather), how far it is to the end of your plotted course, and make your own judgements about fuel economy. Remember though that the faster you run the quicker you use up your diesel.
There is no way round having to babysit the crew and move them to quaters when they get tired, other than using SH3 Commander to dispence with crew fatigue all together as others have said. However on the surface, the game stops keeping track of fatigue at (IIRC) 64x time compression and higher, so while sailing to your patrol grid you shouldn't need to worry too much about it. Managing the game's crew management system is something that you get your head around the more you practice.
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