A ship in the game must be defined in the following files and folders:
Data\Sea with correct name folder; most important ship definition files, all these files (sim, dat, cfg, dsd, sns, dds, val, zon, eqp) must be present and edited correcly for the ship to appear in the game (or CTD!); from what I could see, depending on what you introduce or change, only some files need to be created or changed for a ship, the game will then use the other default files, you may have to copy and rename those files and put them in the ship folder;
Data\Roster\names.cfg where your ship must be with the exact name and unit type; important for single missions and campaigns as well;
Data\Roster\American (or other countries)\Sea to tell the game which textures to load with the ship (dds files located in the Sea folder files) and which are the appearance dates;
Data\UPCData\... for the submarine (aka playable human ship) presence and behavior in campaign
Then, your ship can be used in a
mission file *.mis located in the campaign folder, or in single mission folder or in the single patrol section.
This list is not complete, I'm not a ship builder
Also the list doesn't include all the files and folders for all what comes with the ship which is: the pictures and picture category for the maps and recognition book, environment effects (motion, sinking, trails, etc.), the crew, the weapons that your ship will use and the ship's damage model. Most of this is defined in the Sea folder , but also elsewhere.
I hope this helps, good luck and good work to build your ship!
XS