For the most part, you'd want to use Armor Piercing, but you don't have a lot of that. "Aiming" for a particular location is an exercise in futility from most distances. If you're close enough, the waterline. TMO tuned the deck guns effectiveness down, on purpose, so that a player wouldn't be so tempted to use it, except as a last resort. TMO is a difficulty mod. Another thing to remember about a deck and the Merchants is that if you can hit them, they can hit you... Their "platform" is more stable than yours, just due to the size of the vessel. The best way to "slow down" a surface vessel that is "out in front of you", is to "track it". Figure out what its base course is, then do an end-around on the surface and get in front of it. Plan the attack, and put a torpedo or two into it.
As for the officers on board, that was changed a bit in TMO, but is still not quite correct, but there is a mod out there that lets you choose, but it's probably not compatible with TMO / RSRDC. Editing it to fit shouldn't be real difficult, you just have to watch the differences in the crew slots...
Crew Rank Fix
read the whole thread.