Not a regular scenario. What are you trying to do? If just cruising around with the back window open, you are fighting the design. The hydraulic lifts are helping it down when the window blows against it. You'd need a prop to keep it open. Might as well remove the top before going to the trouble.
I don't drive with my tailgate window open. I think that it puts a lot of stress on the hinges. I'm thinkin if it was meant to be open while driving Jeep would of put some type of locking feature on it.