Start boiling salted water for cooking the pasta.
Make the tomato sauce: Add 1 tbsp. olive oil to a large pot and place the pot over medium heat. Add the finely chopped onion and saute for 5 minutes, or until soft and translucent. Add the minced garlic and saute for 1 more minute.
Stir in the tomato passata, tomato paste, brown sugar, red wine, and balsamic vinegar. Season with salt, pepper, Italian seasoning, and red pepper flakes (if using). Taste and season with more salt if needed. Turn the heat to medium-low and stir occasionally while the sauce simmers.
Make the pasta: Your water should be boiling by now, add the ziti noodles and bring the water back to a boil. Boil the pasta, uncovered, for about 7 minutes, stirring occasionally to break up the noodles. Drain the noodles through a colander, add back to the pot and toss with 1 and ½ cups of tomato sauce. Add 1 cup of ricotta cheese and ½ cup of the shredded mozzarella, stir and cook over low heat until the cheese is melted. Taste and season with more salt if necessary. Keep over low heat just so the pasta stays warm.
Preheat your oven to 350°F.
Make the meat sauce: Add 1 tbsp. olive oil to a large frying pan. Add the ground beef and cook, breaking up the beef as you do, until no longer pink. Season with salt and pepper. Add 2 cups of tomato sauce and stir to combine.
Add 1 cup of meat sauce to the pasta.
Assemble the pasta: Spread the rest of the tomato sauce evenly in the bottom of a 9 x 13" casserole dish. Add half of the pasta and spread it out in an even layer. Sprinkle 2 cups of shredded mozzarella and 1 cup of fresh-grated parmesan cheese over the pasta. Spread the meat sauce evenly on top of the cheese, then cover with the rest of the pasta. Top with 1 and ½ cups of shredded mozzarella and 1 cup of fresh-grated parmesan cheese. (See post for step-by-step photos)
Cover the top with aluminum foil and bake in the preheated oven for 30 minutes. Remove the foil and continue to bake for 10-15 minutes, or until the cheese is melted and bubbly. You can also set it under a broiler for a few minutes to help get the cheese golden brown.
Garnish with chopped fresh parsley or chopped fresh basil, if desired. Serve warm. Leftovers last, covered, in the fridge for up to 1 week.