1. Make sure softtop and window are clean. Don't want to close up the top with gritty pieces rubbing against the window.
2. I find regular car wash soap is good on the top, brush it and rinse it thoroughly. I clean/polish the plastic window with the Meguiar's plastic cleaners and polish.
3. Make sure it is dry before closing down.
4. As top is folded down, lay a clean cotton towel (or flannel sheet, or diaper) into the fold. This way there won't be a plastic to plastic rubbing. It won't hurt to lay a 2nd sheet on top of everything.
5. Make sure the fabric folds are tucked under evenly...not bunched up in the corners.
6. If possible, try to keep a cover on the car, even if it garaged. Moisture can still get into the well.