That sounds like you're headed in the right direction. When you start a career (if you haven't already) you will be assigned a boat. Then you look through the boats on the Battleflags.net site (the download a boat link) and if you find yours, you download it, extract it, put it in your MODS folder and activate it with JSGME. If you aren't familiar with JSGME, look
here.
Again, if the boat that you've been assigned isn't already on the Battleflags.net site, you'll need to request it and we'll need to create it.