Well one way to use the stadimeter while submerged if you're losing the target lock is to pause the game at the exact moment that you have the crosshair lined up with the ship's hull on the waterline. When paused you can use the notepad tools so that way if you can get a lock and get the line on the waterline then you can do it handily.
Another thing to consider is that while U-boats spent much of the war submerged, they were designed to fight on the surface, and to that end the bridge mounted Uzo has a built in gyro stabilizer to facilitate easier observation since the small size of the u-boat causes great rocking. However despite the relative sophistication of the attack scope itself, it lacks any kind of stabilization so it can be hard to maintain a lock that way or to get the stadimeter to be useful in anything but absurdly calm seas.
So if you can, make your observations on the surface. The added bonus of that is that your WO can give you the range and bearing of the nearest target down to the a hundred meters. Useful for quick tracking of a whole convoy.
Hope that helps.
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