Take the three windows out first. But then it doesn't really matter what order you use. Push down on the back corners to give yourself a bit of flex on those tight back corners. I like to fold those "arms" that go down to the back corner up and over the top before lowering it.
Fold it in as neatly as you want as you lower it. Doesn't matter, really, as long as you don't let the "arms" slip out - they'll blow around in the wind.
I've seen people do this very neatly, and if you have the patience, the whole top will fold very neatly in the back. Do it sloppily, and it'll be a bigger bundle above the tailgate. But it's all good.
There should be straps to hold it down. Not everyone uses them.
Treat your windows politely! They will scratch.
My main point? Lower it down. You won't cause problems. After a few times it will be easy, and you'll be able to do it quickly. Definitely not a convertible German sports car, but a good top for our brick of a vehicle.