Welcome aboard!
Once you're in a bunker (when starting a new campaign or patrol), walk to the two guys with ugly baloons over their heads (there are mods that remove these baloons, but they come in handy for now
).
Click on the left guy and select the option to equip the boat. If its greyed out, save and reload. If I remember correctly, you'll find the emblems in the right most tab. There are some emblems in vanilla game, the mod you installed adds a lot more. Some cost some renown, the other ones are free. Once you sail out of the pen, you'll find your emblem on the conning tower.
Good luck and good hunting!