Bring a large pot of water to a boil. Add 1 tablespoon salt and cook the pasta according to the package directions until al dente.
Drain the pasta, return it to the pot, and stir in 1 tablespoon of olive oil. Set aside.
To a large skillet over medium-high, add the remaining tablespoon of oil and then brown the beef or Italian sausage for about 5 minutes. Add the chopped onions and cook for another 5 minutes until the onions are soft.
Pour the marinara, tomato puree, and Italian seasoning into the skillet. Stir and bring to a simmer, then reduce to low heat for about 10 minutes.
Add the sauce to the pot with pasta and mix in 2 cups of mozzarella, ricotta, and parmesan cheese and stir it all together. Transfer the pasta to a 9-inch x 13-inch baking dish. Top with the remaining 2 cups of mozzarella cheese, or more if you desire.
Bake at 350 degrees F for 20-25 minutes. Allow the pasta to cool for 5 minutes before serving. Garnish with more parmesan cheese, fresh parsley, or chili flakes for some heat.