@kabura : You probably don't want to know how we did it as we should have used real 3D instead of 2D art with 3D gameplay.
Anyway here's a walk through hell:
Godot engine handles isometric tiles on its own, with layers allowing us to paint a 3D island of cubes easily.
However when comes the time to add buildings they need to follow the same 3D logic as the cubes, sometimes an upper layer has to be drawn behind it, sometimes it has to be drawn in front. The only way I could think of to do it with 2D assets is to divide the entire asset in cubes:
Aseprite_EWKqi2Lez7.png
See this innocent looking factory?
Aseprite_XU5ODWVzbb.png
Now we need to imagine it like a pile of cubes.
Aseprite_MOxrXfCH7H.png
We'll start from the upper layer as it's the most visible one, the one overlaying all the others.
Aseprite_LKO5cXa6U2.png
Then we select the front cube, for the same reason.
Aseprite_EX6LzNmx2v.png
And there we have our 5th lvl front cube.
Tileset.png
We can now add it to the tiled set and draw it at the right location on the right layer (current layer + 5 level).
And why am I doing that? What was I thinking?
Don't do that. Use 3D.