- Try to get the numbers in the bonuses more in the middle
I have been trying to fix this, do you know how?
Since you can't set center points for bonuses, you have to change the bonus. Either the shape itself or add a new shape. Basically, you make a second box/shape that is made in a color that hides it then make them part of the same bonus. In this way you can 'move' the center point.
Seeing your map through, I would try to scale up the 'bonus map' first, since that is simpler and you have space. Also, never done ^ that myself, so my description is a bit sub-par.