if you are using a windshirt like its "meant" to be used ... size it snug enough that you wont be flapping in the wind like a flag
especially with active pursuits ... the snugger it is the better its "breathability" (theres a reason why gore requires its active shell to be snug) ... and the less it gets in the way
usually just large enough so that it can take a fleece or UL down jacket under ...
when at quick stops simply put the puffy over the windshirt ... sure you lose a bit of "warmth" vs putting it under ... but you arent going to be faffing around taking your windshirt off, putting on the down jacket, then putting back on the windshirt when its only a short time ... youll lose more warmth with that process, not preserving the built up body heat ... and in windy conditions, a recipe for losing a layer
in camp you can put the light puffy under the the windshirt ... or if its a larger puffy, put it OVER ... for rain as someone has mentioned it makes more sense to size the RAIN JACKET to fit over everything, rather than the windshirt, and simply put that on