Large ship (anything over 10,000 tons min, the more the merrier) tend not to move up and down as much as other ships. They still do so its really tricky to use magnetic setting for them. If you've got a really juicy target you can gamble and set all 4 eels to a magnetic setting around 0.5-1.5 meters under the regular draft. As there's a delay in the time between each one launches (albeit only a few seconds) it can be just enough for 1 of the 4 to get a good magnetic detonation and potentially 1 shot sink it or kill its propulsion (or at least slow it down) while hopefully one of the others scores an impact hit. Depending on the draft setting for impact onnly anywhere from 2-5 meters is great, you'll usually score a hit on it and hopefully slow it down so you can get closer to make a more precise shot.
While bad weather makes it harder to target (obviously) it is to your advantage in the sense that you have the upper hand in maneuverability as 50m below your sub still drives the same as if the sea were calm while the escorts have to deal with all the havoc going on topside. Especially in a convoy you can run around at flank to maneuver and then hide under a large tanker or cargo to hide from the escorts, then once reloaded move out to position yourself for the next attack.
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