Preheat oven to 400F.
Bring a large pot of water to a boil for the pasta.
Prepare both sauces first, then salt boiling water and undercook ziti by 1-2 minutes, just shy of al dente. Reserve 1 cup of the starchy cooking liquid just before draining ziti.
For the green sauce, melt butter in a pot over medium-high heat. Whisk in flour, cook 1 minute then add milk. Cook to thicken to coat spoon; season with salt, pepper and nutmeg to taste. Keep warm, covered over low heat. In a food processor, combine herbs with nuts, garlic, half of the Parm a couple of handfuls salt and pepper. Add EVOO and pulse into very thick paste. Reserve.
For the red sauce, heat a saucepot over medium-high heat with EVOO. Add garlic, herbs and red pepper flakes, and stir 2 minutes. Add tomato paste and stir until fragrant; add wine and reduce by half. Add onion, bay and canned tomatoes; break them up and season with salt and pepper. Stir in basil, reduce heat to simmer and cook sauce 30 minutes partially covered, stirring occasionally. Remove onions and bay.
Toss half of the ziti with red sauce, half a cup of starchy water and the ricotta cheese. Transfer to large, deep baking dish.
For the green ziti, stir pesto into the white sauce, turning it green. Toss remaining ziti with half a cup starchy cooking water and the green sauce. Carefully arrange the green ziti over the red.
Top the entire casserole with mozzarella or provolone and the remaining 1/2 cup grated Parmigiano-Reggiano cheese. Bake until bubbly and brown, about 15-20 minutes.