Suggestions on setting
 

If you encounter a convoy when there are waves cresting over your conning tower on the surface, what type of settings should I be using on my fish? I had several fish underrun their targets, which I understand is historically accurate, but is there anything else I should be playing with in regards to depth, etc?

In that sort of weather, assuming it isn't going to clear up and you want to attack in it, then I would go for the shallowest setting possible and fire three with a bit of spacing on them so the chances of them all 'troughing under' would be minimised, as it's going to play havoc with depth-keeping on the torpedoes. Go for contact detonation rather than magnetic and try to get them to strike at 90 degrees to the side of the ship, to avoid a dud from a glancing blow. Make sure it's a worthy target though if you chuck that many fish at it.

:D Chock

Well, I tried the opposite thing on depth settings, I was shooting at at Modern Freighter, and set the eels to run at 15 ft, thinking that they would avoid the worst of the waves by running below them, sadly it seems they all ran TOO deep, as I saw 2 of them run right under their target.

So next time I should shadow and wait for better eel weather?

Running too deep is historical so early in the war you need to set challow and contact. Later in the war, you can set what is correct for the target and magnetic regardless of the weather.
-Pv-