I think I've only had any luck doing this by getting very close (submerged) and using a magnetic fuse on an eel set to run at maximum speed. And then I try to be coming in perpendicular to the ship's general course, i.e. the more or less straight line across which she is zigging and zagging. And then I try to fire when she's starting to make a 'zig' towards me rather than in the other direction.
I don't know if that's the "proper" way to do it, but I seem to remember it working. Could've just been luck.
What I prefer to do if I can is just submerge, lower my scope, and continue to run parallel to her general course, staying as far ahead of her as I can while keeping within easy range of setting up a good shot once she stops zigzagging. Which they usually seem to do eventually.
Of course if the ship is fast enough that I can't stay with her submerged, I'll work my way out of good visual range and then resurface and try to run parallel to her general course and overtake her again without getting close enough to be spotted, and then move in for the kill again (submerged if necessary).
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