Well, all the ships are compacted into an install program, so you don't have to worry about inserting ships into it. If you read the readme however, you will notice that if you want to save the original designs of the ships, they you should remove them from the ship files and put them in another folder whereever you choose on your harddrive.
However, to install the ships in the Mod, all you do is click the icon, and the install program pops up. Did I misunderstand the question, or is this what you were seeking?