I've taken the liberty of making a reservation for you over at
WASSAT, the WernerSobe Advanced School of Submarine Attack Tactics, where you can learn how submarines set up and attack their targets with full manual settings. However, I'd recommend you set phasers to "wimpy" for awhile and learn to handle your boat.
That way you can learn to stalk the targets and when you get close, just put the target in the crosshairs and push fire. Knowing the underlying principles from Werner's movies will make the process much more enjoyable.
Be advised that adding Reflections on the Water early-on will not make your game more difficult, just more beautiful, and the same goes for Natural Sinking Mechanics. I would heed AVG's advice and play the game naked (preferrably with a friend:p, you know, a first mate) until you can appreciate what these great mods bring to the table.
Leave some targets for us and don't hesitate to ask questions!
