There is a bug in the game, relative to Steam Workshop, and some of the mods may not appear in game.
Check this thread here with the PDF:
https://forums.galciv3.com/491562/galciv-305-bugs
It's item 19 on his list.
Once you do that, you will be able to use the ships you got on Steam Workshop.
Doesn't matter if you play Terran, you can still design your own custom ships. What you can't do is, say, have the Terran Corvette look like something else. But if you're really attached to the name, it could be "USS Corvette" and it would work.
At lower difficulty levels, the AI will use the default ship models. At some higher level of difficulty (I can't remember which), it is supposed to also look through your ship designs and use them appropriately.
Anyway, once you have done this steps, go to the ship designer, design a new ship, select the models from the list and save it with the name you want (can be the same name or anything else you want). Go back at the designer, you will see your ship model, use that design then add the engines, weapons, defenses, modules you want and save it again under the same name.
It will not replace the default designs of the ships for the faction you play, but it will let you create any ship you want from these hull designs.
Creating a custom faction, you could mimmick the Terrans and have your own pre-established fleet, but I'm not sure how that works, I haven't played much since before Crusade. 
