Clay, the quality towel over the window is a good practice, and will prevent scratching of the new plastic. Also, you should check into buying some 303 protectant for the top and the window: http://www.303products.com/main.php
Just some added protection... brought my poor top back to life, and it's lasted 6 years where I thought I was going to have to replace it the first year after buying the car...
As far as I know Jim C is correct. Non zippered plastic window was all that was originally offered. Now the same, a zippered option and a split glass (hinge seam in the middle) options are available. Another great source of info and products is: http://www.convertibleparts.com/ Very helpful for any questions you may have, willing to help!