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The "Point Defense Cannons" should fire away automatically against any enemy torpedo or fighter at a max range of 40. They should work on any ship. I have played the game many times and never encounter any noticeable problem with them.
One player commented once that sometimes at some angles they do not fire. I cannot explain why. Try to put them on a different slot to see if that makes a difference.
I am pretty sure that if the enemy fire two torpedoes and you only have one PDC, you will be hit at least once. Also the PDC can get damaged (or any component that can affect the PDC like “reactors”) and therefore not be able to function.
I reloaded campaign 2 and got into the ship installed the PDC and it worked just fine. By the way the only difference between Mk1, Mk2 and Mk3 is just tonnage capacity.