
It looks very simple. First of all, how would you represent such a level? That's easy you say, just have a two dimensional array of values. Each value represents what kind of tile there is in that space. Just like in a 2D tile-based game seen straight from above, X coordinate could increase to the right and Y coordinate down, except at a slight tilt.

This is not the only possible coordinate system of course, but this way the tiles can be drawn in the traditional loop of increasing X and Y, and still occlude each other correctly. That's it then? All the complexities of an isometric engine solved. Not quite.
To be continued...