Place a large pot of water over high heat and bring up to boil to cook the ziti. Once boiling, add some salt and the pasta, and cook just shy of al dente. Drain thoroughly.
While the water is coming up to a boil, start the red sauce: Place a medium-size saucepot over medium-high heat with 2 turns of the pan of EVOO, about 2 tablespoons. Add the onion and garlic, and cook, stirring every now and then until the onions start to get tender, about 3-4 minutes.
Add the tomatoes and smash them up into small pieces with a potato masher or with the back of a spoon. Add the basil and season with some salt and pepper. Bring up to a bubble and simmer for 15 minutes.
Once you have the red sauce working, make the white sauce: Place a medium-size saucepot over medium heat and melt the butter. Add the flour, stir to combine and cook for about a minute. Whisk in the milk, add the bay leaf and season with some salt, pepper and a couple of grates of nutmeg. Bring up to a bubble, turn the heat down to low and gently simmer, stirring frequently, for 5 minutes. Remove the bay leaf and discard.
Combine the cooked ziti with the red sauce in the pot the pasta was cooked in and transfer everything to a baking dish. Top with the white sauce. Sprinkle the mozzarella and grated Parmigiano over the top, transfer to the oven and bake for 25-30 minutes.