Folding the roof down incorrectly can crease the rear window and/or quarter lights with the potential effect of splitting those windows. At the very least the creases are likely to diminish your visibility.
Many people 'cheat' on the rear window by unzipping it and laying it down first, this certainly helps extend the lifespan and is better than introducing a crease, but it doesn't help those rear quarters.
I would like to thank Jay Human for allowing me to reproduce the following article, displayed on his website, which graphically describes the correct method of lowering the hood.
Step 1: Detach The Hood From The Frame.
The hood is attached to the middle frame bar, via a Velcro strip (see Fig 1.0). This can easily be detached.
Also unclip the poppers attaching the hood to the car body and release the front locking handles from the windscreen surround.