You might want to try this. For the first attack set the eel depth to 1m, max speed, below the keel. Get as near to 1000 m and bow angle 90 as you can, lock on the Rodney with the 'scope, and open the torpedo doors(Q). Then unlock the scope and shift the 'scope so the crosshairs are resting on the middle of the front three turrets, then send an eel on the way.
I'm not sure that targeting by clicking on the boxes in recognition manual is enabled in GWX for non-vanilla ships (RTFM i suppose:hmm: ).
I'd advise this as
a) the stern rises substantially making a magnetic setting more like guesswork for the disabling shot advocated by some, and the sea is very stormy you say?
b) Stormy sea may cause a premature, while this method means you still have another chance with the second bow tube.
b) the magazines supplying three turrets must have been huge! Put all the belt armour you want on it First Sea Lord, 'cause we found one of your magnetic mines in the last war!
d) You still have a stern tube to sink The Hood on the way home!
On second thoughts, send both eels in a spread, spread angle 1 degree, target as previous. Two torps under the magazines should be a mortal blow