Hey Rob GW1.1a uses the NYGM damage model which makes ships sink as if they are flooding. You need to fire your torps at different sections of the ship and when useing the deck gun you should fire below the water line. For a small merch you should be using no more than 2 torps aimed at different sections. Thn wait for a while say 20 mins game time then deside if you are going to need the deck gun.
When using the deck gun i useualy fire 10 or so shots and then wait for a while to see what effect that has.
Hope this helps