1) Never store them with plastic against plastic. Whether you roll them or lay them flat, always put fabric of some kind between them.
2) Never use window cleaner on them. It will cause them to cloud or become yellow. Bestop makes an excellent cleaner and protectant. It's pricy but worth every penny.
3) Always rinse away grime before cleaning and use only clean micro-fiber towels on them.
4) Never scrape frost of ice off of your windows
5) A cab cover or even a tarp will help protect them from the elements ie. sun, snow, frost
6) (and 1 I learned the hard way) Never travel at highway speeds with the rear window rolled up. You are better off just removing it and throwing it in the back.
Hope this helps