So of course I went to the trusty internet to do some research and found I was right. But is there really a right way or wrong way? I decided the best way to go is with the company who makes the soft tops as seen in this video.
This picture shows how that fellow Jeeper had his soft top. In the instructional video this is not the proper way to lay the soft top back on the tailgate. As you can tell in this picture the side bars are parallel to roll bars. They need to be resting along the body of the Jeep.
you need to make sure the fabric of the soft top is pulled away from the bars.
When you are putting back your soft top in the first position where it lays right above the passenger seats you want to make sure the fabric is not squished between the bars.
The Perfect Jeep "W"