Here's a couple of pictures of the Coleman Laramie. Although this is not a Jayco brand, it provides an example of how a typical pop-up should look and might help you figure out what's wrong with yours so you can correct your problem.
Notice that the canvas is arched above the rear window.
As you can see, the arched aluminum frame in top of the rear window fits into the seam of the roof and rear window canvas. The aluminum center roof support pole (sometimes referred to as a "candy cane") is adjustable to allow for variations in the canvas.