I am sure you realize that there is a third way, which is really just the “average” of the other two. Just take the cooked macaroni tossed (mixed) with the cheese sauce (from the first way) and pour it into a greased casserole. Top it with additional cheese (shredded sharp cheddar preferred) and bake it just until the top browns a little.
Here in Western Massachusetts we do it the above way…but…we sprinkle bread crumbs over the top before baking it. The cheese bubbles up through the bread crumbs and forms a nice “crust.” Yummy!