Best angle of view
If the top board is to high, it will be hard to discern your options on that level.
You need to be able see through the top of the board and look at your other chess pieces on the bottom board. Therefore, the best set-up would be:
Top Board is at table height and the
Bottom Board is Below table height by about 6 inches (15cm).

That's Me, 3DPG, playing Chess in 3D
← Table Top level

← Bottom board is below table top level by 6 inches (15cm)