If you have a package with Two Sets of Straps, they are for the Soft Top.
The Velcro Set is used to hold the bars down when the Soft Top is folded, and also used to hold the bars down when the SunRider is folded back.
The other Set with a Snap on it, is indeed used for the rear window when it's rolled up. I wouldn't recommend using it however, as it tends to leave two nasty wrinkles on your Plastic Window.
If, by chance, you have a Hard Top, then this post is funny! Why? Because I see more and more posts from Soft Top Owners, asking where the Straps are for their Soft Tops. Seems like the Dealers are playing Musical Straps with these packages. I had to contact my Dealer twice to get mine, finally. I contacted the Sales Rp and Parts Dept, and somehow, I wound up with three sets. I guess you can never have too many!
'09 Yellow JK X
-Sony CDX-GT540UI Head Unit
-Alpine SPR-17C Coaxial 6.5" Speakers
-Alpine SPR-17S Component 6.5" Speakers With Tweeters & Crossovers
-Rockford Fosgate Punch 400W 4-Ch Amp
-Factory Half-Doors & Full-Doors
-Michelin Latitude Tour Tires
-Black Rock Viper 900 Tungsten 17" Wheels
-Pre-Runner Light Bar
-KC-127 6" Fog Lights
"The Floggings will continue until Morale improves!"