I have mine in the bottom holes at the rear, and the higher holes in the front, for a slight tilt. Suits my short legs better than perfectly level would. Ignore the top hole on the left side bracket, there is no corresponding hole on the right. I have no idea why H-D made it that way, but it's been like that for a long time. With my bike sitting on a center stand, the left side board is 1/2" higher relative to the floor, front and rear, than the right side board. It's probably got something to do with the fine tolerances Harley employs in all their parts including the frame and board supports. Until you mentioned it in this thread, I'd never measured them because in normal riding I don't "feel" a difference. I didn't try to rig up something to measure the height difference side to side from a different reference point higher on the frame.
Jerry