It's not confusing, I've come across that too. If the animal and place they're on/in is purely decorative, distributing invisible blocks does the trick. You can also try and select some specific element of your tileset that fits well; a larger piece of grass, a corner -- when I tried to build screens that included walking creatures in the air, I was using a tile that was just a small, small solid triangle on the corner of the tilespace, it looked alright. If you want, you can post a screenshot and ask for more specific solutions.