In the 6 to 8 quart pot, bring water to a boil. Add some kosher salt and the pasta and cook according to package directions. Drain well.
***While the pasta is cooking***
Warm the milk in the 2 quart saucepan. Melt 6 tablespoons of butter in a large (4-quart) pot and add the flour. Cook over low heat for about 2 minutes, stirring with a whisk. Continue whisking and add the hot milk and cook for another minute or two. The mixture should start to thicken and get smooth.
Remove from heat. Add the Gruyere, cheddar, pepper, and nutmeg. Add the cooked macaroni and stir well. Pour into the prepared 3-quart baking dish.
Arrange sliced tomatoes on top. Melt the remaining 2 tablespoons of butter, stir them with the fresh bread crumbs, and sprinkle on the top.
Bake for 30 to 35 minutes, until the sauce is bubbly and the macaroni and breadcrumbs are browned on the top.
Variations: To make ahead, put the macaroni and cheese in the baking dish, cover, and refrigerate until ready to bake. Put the tomatoes and bread crumbs on top and bake for about 40 to 50 minutes.