Building exactly what you want underwater, above water in sand on a layer of dirt. So all three dimensions. You'll just have to add the permanent layer all.
The first way is with depth: adding overhangs on to roofs, varying the materials you use, and making sure there aren't too many flat areas on your houses.
Some of the best Minecraft houses are designed in a biome with mountains. These styles of houses are favorites among those who enjoy breathtaking views.