Preheat the oven to 350 degrees F. Coat a casserole dish or 6 8-ounce oven-safe ramekins with cooking spray.
In a large bowl, combine the cooked pasta, ricotta, marinara sauce, ½ cup of the mozzarella cheese, and ¼ cup of the Parmesan cheese. Stir to mix well. Spread the pasta into the prepared dish or ramekins and sprinkle evenly with the remaining ½ cup mozzarella and ¼ cup of the parmesan. Bake until the cheese has melted, 15 to 20 minutes. *Best when eaten immediately.
For the marinara sauce: Heat a large pot over medium heat. Add the oil and swirl to coat the bottom of the pan completely. Add the onion and garlic and saute, stirring occasionally, for about 7 minutes, until browned. Lower the heat if they begin to burn. The more color that develops on the onion and garlic, the more flavor they'll add to the finished sauce.
Once the onions and garlic are tender and caramel in color, add the crushed tomatoes and the tomato paste and stir until the mixture is smooth and well combined.
Add the remaining ingredients (oregano through pepper), stir, and bring the mixture to a simmer. Lower the heat to the lowest setting, cover, and cook for 30 minutes, stirring occasionally so that the bottom does not burn. Serve.