The program is shipedit. I don't have a link but a search of the forum might find it. However if your just putting a ship in and not modding the stats. I find it easier to open shiplist with word pad. You will find that the same model is being used for as many as a dozen different designations. In the shiplist, scroll to the right, about halfway across you come to an entry like this.
assets/models/fff/fff.mod That is what the game is using to point to a folder and mod file. This is saying to use the fff.mod in the fff folder. If you want to drop in a ship that has a mod called norway in a folder called norway. All you need to do is change this part of the entry to assets/models/norway/norway.mod and thats it. Presto. What I do is I rename my ship mods and folders using ship class and numbers. So I have fff2, fff3, fff4 and so on. Then I don't need to type in long names like norway. I just change assets/models/fff/fff.mod to assets/models/fff2/fff2.mod and I am done. If you make a typo you are screwed until you catch it. But you can make a typo in shipedit just as easy.