Just for the shallow water patrol missions, I would only attack at night or in bad weather when in / near shallow waters. If you do not have a deep area in your patrol zone to help you "hide", and your "patrol time" is continuous, I do what you do, and stay submerged in the area, in the deepest spot there is, during daylight hours, until the time is fulfilled and the mission objective completed. I come up for air at night and surface patrol, making certain I'm back at my "parking spot" for the daylight hours. Not "realistic", but the game doesn't allow too much "realistic" anyway. After completing the objective, I go elsewhere (deeper, rougher water) to do the sinkings, if I don't have any yet...
