It doesn't help if you've trying to do it totally blind, but the 2 open square holes go on top, once I figured that out I've never had any issues plugging them in correctly. The only one I have issues with is my keyboard because the pcb in the plug is black and the it's a little hard to tell which side is the open holes and which side is the black pcb.
Vertically aligned motherboards are hard to judge what "up" is. Usually up is where the expansion boards are plugged in. But not all computer users know how a computer looks inside.