Mine is a 2012 so not sure how much the top has changed. I keep by back window section on year round (it helps cut down on dust in summer)so I fastened that with zip ties trimming the excess. I also connected the top to the roll bar with zipties as well as I roll the top back onto the roll bar when I want open air. This allows me to snap the top over the passenger area in a minute if needed. If your top still has internal type flaps that connect to the roll bar tie them on the far back side to make it a bit tighter. Here is what I did to make the top a bit tighter and how I roll and store it.
As for the zipper leaving marks. 3M makes a clear plastic film that can be applied to the body in this area that will aid in the zipper not scratching the paint.