Problem aligning tiles in an isometric map

I’m new to Tiled, and I need this for a isometric game I am making with LibGDX.
This is the tileset I am using:

Since the tiles are extruded on the bottom, this creates problems with alignment in the editor that I don’t know how to fix.
This is the result, and how it should be instead:

Is there a way to make those tiles work?

Build one set of tiles without the sides to represent the floor.
Build another set of tiles that represent the sides.

Indeed you’ll probably want to put the tiles in different tilesets depending on their size. Placing the walls correctly will be easier if it’s a single tile rather than being cut in halves.

But the main problem in your screenshot with the tile alignment is due to choosing the wrong tile height when creating the map. You can change the tile height of the map by going to Map -> Map Properties. When you change it there you can see the effect it has on the map immediately.