MAKE THE SAUCE: In a large skillet set over medium heat, heat the olive oil. Add the onions and garlic and season with salt and the red pepper flakes. Cook, stirring from time to time, until the onions become translucent, 3 to 5 minutes. Add the tomatoes, sugar, and oregano and stir to blend. Cook, continuing to stir from time to time, until the tomatoes start to smell cooked and the raw garlic mellows, 18 to 20 minutes more. Taste for seasoning.
COOK THE PASTA: Bring a large pot of water to a rolling boil. Add a generous handful of salt; the pasta water should taste like seawater. Add the pasta and stir with a slotted spoon to make sure it does not clump or stick to the bottom. Cook until al dente, 8 to 10 minutes. Reserve 1/2 cup of the pasta water, then drain the pasta in a large colander.
COMBINE THE PASTA AND SAUCE: Add the hot pasta right from the colander to the skillet and toss to coat with the sauce. Shut the heat off and allow the pasta to rest for 10 minutes-ideally the pasta is nicely coated with the sauce but it still looks saucy and not dried out. If it becomes too thick, simply thin it out with some of the reserved pasta water.
BAKE THE PASTA: Fill an 8.5 x 11-inch baking dish with half of the ziti, sprinkling half of the mozzarella and Parmesan over the pasta as you fill the dish. Top with all of the remaining pasta and cheese. Bake until the top browns, 15 to 18 minutes. Switch the oven to broil and broil the ziti until the top is browned and the sauce bubbling, 2 to 3 minutes.
SERVE: Tear the basil and sprinkle over the top. Serve family style.