The clips fit in the holes you have highlighted with the red ring from above. You can see them in the pdf that is on this link http://www.zpost.com/forums/showthread.php?t=1215892.
Basically they clip in from above, it's a bit difficult to access, but can be done by moving the fabric flap that covers the roof tray. Also I think there should be two on each side, the front ones I attached by going from the front of the car over the back of the seats into the roof tray area.