Floors override each other, but you can place walls and fences/tables on top of floors. The way the system determine what type is a tile is by looking at its position in the tilesets. Head over to the database and in the tilesets tab.
Tile A1: All animated floor tiles (usually water tiles)
Tile A2: The first half vertically is for floor tiles (ground floor usually). The second half vertically is for anything that goes on top of floors (grass, fences, tables, holes, etc.).
Tile A3: Walls and Roof
Tile A4: Walls
Tile A5: Miscellaneous
A1 And the first half of A2 can't be on top of each other.
The rest can go on top of A1 and the first half of A2.