If you take a clean plush towel and lay it in as the top folds (the window fold back on itself) you will prevent scratching. And to actually preserver the window and keep it clear as well as keep the top protected from the sun and the elements use 303 protecant products and cleaners: http://www.303products.com/ You can usually find them at marine supply stores etc. You will be amazed at what it will do for an older top and window too.

Yes, go with the plastic...

Brett!