A new top for the Jeep would be really pricey, and my husband didn't have a need to remove the window regularly. So, I picked up some fishing line and used it, along with an embroidery needle, to sew the window onto the Jeep top.
I started in the lower right and worked my way around, just looping the line/thread around the zipper to hold it.
It doesn't look great, but the outer flap covers it nicely, so it really doesn't matter:
However, we did want the ability to open and close the left side so we could add and remove larger things from the back of the Jeep. So, I stopped sewing in the upper left corner, and picked up some black velcro.
The velcro is officially "new sew," meaning it is self-adhesive. I'm pretty sure it wouldn't stick very long on the back of a Jeep, out in the weather, though. So, I used the fishing line to sew the velcro pieces down the left edges.
Again, it isn't the prettiest job around, and it doesn't really have to be: it gets the job done. The flaps cover the velcro and stitches nicely, and so far it's working great!