Yes, all clips have to be installed before the glass goes in. The clip will seat against the bottom of the frame on the a-pillars and the top crown. The lip for the bottom clips is deeper so you will need to look at the other clips to see how close they are to the outer lip and mark the bottom ones the same so the molding can grab on to them.
If you still don't understand it will be crystal clear when you go to do it.
