[Dave S.]

For keeping the window from scratching, probably the single most important thing is to make sure their is no dirt or dust on the window before you put the top down, and never wipe a plastic window with a dry cloth.
I carry a plant spray bottle with water and a soft towel in the trunks of my two convertibles with plastic windows. I spray the window and wipe it clean every time before putting the top down and I've had Triumphs for over 25 years with no scratches in the windows this way.
Even when clean, if the window folds so the plastic is rubbing against itself, it will leave a mark. Felt or soft towels on the windows works really well to protect them, but you still want to make sure they are free of dust or they could still get scratched.