Step 1: Go to
http://www.battleflags.us/, click on "Download a Boat", find the skin for your specific boat and download it.
Step 2: Get a free image editing program like GIMP or Paint.net.
Step 3: Copy and paste the appropriate kill flags onto the NSS_GatoTower_T01.dds (or whatever class of boat you're working with), and make a duplicate of that same file for NSS_GatoTower_T02.dds.
Step 4: Install the mod with JSGME like usual.
While the original site doesn't appear to be up and running yet, I'm willing to help out and do a few killflags for people not comfortable with editing the dds files themselves. As long as the boat's base skin with the logo has already been made, that is.