But how do you handle the perspective? See my example, that's my doubt:
The first is a square turned into a cube and each side (the top flat) has 64px so the height of the triangle is 90.5px. However, the second one is isometric but with perspective (looked from the mid top) and then all sides have it's sides changed (from 2d view) to something smaller than 64px. Based on this, my height calculations, which would be my reference for every position, is basically lost I guess.
Could you explain me that please?