Preheat your oven to 375°F (190°C). Bring a large pot of salted water to a boil. Cook the ziti pasta according to the package instructions until it is al dente. Drain the pasta and set it aside.

In a large skillet, heat olive oil over medium heat. Add the chopped onion and sauté for 3-4 minutes until soft. Add the minced garlic and cook for 1 more minute. Next, add the ground beef, breaking it up with a spoon, and cook until browned and fully cooked. Drain any excess fat. Stir in the marinara sauce, Italian seasoning, red pepper flakes if using, salt, and pepper. Let it simmer for 5-10 minutes so the flavors come together.

Remove the skillet from heat. Mix the cooked pasta into the meat sauce, stirring well to coat all the pasta. In a large baking dish or oven-safe skillet, spread half of the pasta and meat mixture evenly. Spoon dollops of ricotta cheese over this layer, then sprinkle half of the shredded mozzarella cheese. Add the remaining pasta mixture on top, and cover it with the rest of the mozzarella and Parmesan cheese. Bake uncovered for 20-25 minutes until the cheese is melted, bubbly, and lightly golden. Let the dish rest for 5 minutes before sprinkling with fresh parsley and serving.