I see what you're trying to do, you're trying to show the interior of the ship and the water at the same time. The set isn't made for it but there are a few ways you could make it work. They're all a bit complicated though, because they're all workarounds to the way that Ace handles tiles.
Way #1: Make all the slanted tiles into animated A1 tiles. This is by far the most complicated method, but it gives you the most freedom for mapping other things on top. You'll need to have an extremely thorough handle on how the A1 tiles work and be very comfortable with shift click mapping. Basically through those two things you'll be forcing the A1 tiles to work like regular tiles and not autotiles.
Way #2: Make the slanted tiles into A2 tiles. This is almost exactly like the first method, only you're replacing the transparent A2 tiles with the slanted stuff. This is the same difficulty and effort as the first method. Basically this is for if you don't want to replace most of your A1 tiles but don't mind replacing the A2's instead.
Way #3: Use the slanted tiles from D, map stuff on top using events. RECOMMENDED. It uses more events which can slow things down if overused but you don't have to fight the editor as much and you don't have to edit any tiles.
Way #4: Combine the water and slanted tiles and place them in A5. I do not recommend this method. If you do this the water will no longer be animated. However, if you have a lot of stuff you want to map on top of the slanted tiles and you don't want to mess with much tile editing and crazy mapping it is an easier way. I just don't think it would look very good.
