In rough seas that are too difficult to attack in submerged try to aim for a surface attack at night,or decks awash if it is a light night compared to a pitch black one.Ideally the attack should be made at between 1-2000m (light conditions permitting) bow on so your profile is narrower and with impact tips set high (as Jim mentioned),NEVER use mag tips in those conditions!.
I personally like attacking in storms myself.
Master the storms and you master the seas!
And always remember,
BE MORE AGGRESSIVE!! (sorry Jim hehe)