Doctrine question: when to submerge on patrol?

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Is anyone familiar with real-life doctrine on when US subs ran submerged and when surfaced?

I have come across a few websites that said that at the start of the war, subs had strict orders to stay submerged below 100 feet within 500 miles of an enemy airbase, in order to avoid being spotted by aircraft (http://www.valoratsea.com/subwar.htm). I'm presuming this means during daylight, and then they would patrol on the surface while recharging batteries at night. I also came across an entry(http://www.navyhistory.com/Submarine/troutI.html) that says that during a prewar practice patrol, the sub remained submerged from 0500 to 1800 each day (although this would have to be adjusted as you change longitude).

The question is, what do they mean by "patrol" -- do they mean once you are ON STATION and seeking contacts? Or do they mean any time after you leave base? I see two problems:

(1) what about when you're traveling to reach station? Do you travel during the night and go slow submerged during the day, effectively cutting your travel speed in half? Do you start doing this once you get within the enemy air zone?

(2) what about when you find a contact and need to get into position? Speed is necessary, are you (doctrinally) allowed to surface to flank and then resubmerge? Even shadowing submerged until sunset, it might be pretty hard to keep up with a good contact without running out of batteries, which you will REALLY need once you do your attack run. And if you can't flank on the surface, what's the point of calling it "flank"?

I also read that US subs were doctrinally supposed to fire from deep submersion using only sonar contacts, but this worked very poorly and successful commanders basically started ignoring this and shooting from periscope depth with visual contact. To what extent did aggressive commanders follow the surface/submerge patrol rules as well?

From reading "Das Boot," it sounds as though U-Boats ran on the surface frequently while in range of enemy aircraft, and crash dived when they sighted one. They probably had little choice, since the moment they were out of harbor they could encounter aircraft, at least once the war got going. If they did the travel-by-day, submerge-at-night thing, they'd never get to their patrol zone. Or do I have it wrong?

I'm always tempted to run on the surface until I get to my patrol zone, and crash to avoid planes when I see them. In SH3, I really only submerged to attack or do sonar checks, or when I was transiting Scapa or the Channel where I'd get buzzed every 10 seconds. But I realize this is because I'm playing a game and my life isn't really at stake. I have a feeling I'd be a lot more cautious and a lot less impatient if the bombs and bullets were real, and my first mistake would be my last.