I laid everything out as per the pic below. I decided to move my empties up on the z access so they were easier to select. The heights are dependant on amount of items they contain. I also categorised everything separately.
Sometimes, empties are used to control aspects of the construct. Then it will be important to have them at certain locations. For example, at the origin point.
But for the chessboard challenge, it is ok.
You can change the shape of the empty, or even create your own shapes.