Keep in mind that the blue box version gets flipped in game. The only workaround ive found is flipping it and making sure any static props are set to simulation disabled. I haven't found a good way to place players around them.
I made one recently and was able to get the well deck and hangar deck set up. I stopped short of adding ACE to the flight deck but with some trial and error you should be able to place some air assets up there.
https://drive.google.com/open?id=0B2c37fNovV4iWlQwRzh4VjkwWG8