GoDot and tilemaps

GoDot and tilemaps

What is the best practices on layering tilemaps?  Lets say I have a world and there will be tilemaps for water, earth, trees, buildings and maybe even multiple layers in a building because there are multiple floors.  Is the best way of accomplishing this feat using multiple tilemaps?  I am thinking the water would be the bottom, then the ground layer, then the floor of the buildings, then the tables of the buildings and so on.  Or there a better way to do this hierarchy?