Depends upon the time frame of the war. Early on, running surfaced during the day and evening when they were out of the range of British planes. Later on, submerged during the day and running up top at night to charge the batteries was the deemed "safest" tactic but that did not matter much when the newer radar systems were installed, night turned into day so to speak and it was almost impossible to spot a plane at night.
Diving and staying submerged was useful to do a sound check with the hydrophones, as sound traveled farther than what they could see.
As for sitting still in a harbor than raising your scope and being detected, well the game was not made perfect. There are many situations where there is no way in he11 that an escort could have picked you up and somehow they do, hard code problem. Though there are conditions with sea water which disturbances upon the water glow (phosphorescence is the name I believe). Rough seas are much worse for detection, crystal smooth waters can be your death.
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