It depends
In the winter/fall when stopped for a break/lunch/etc- my puffy goes over the top, this is simply for efficiency sake- it's quicker to don/remove. Keeps the heat in while stopped w/o much fuss. If I'm going to be glassing (or something that's going to take awhile) I usually layer it under a windshirt or hardshell. If there is a lot of wind or precip- it always gets layered under.
