01 - Preheat oven to 375°F. Lightly grease a 9×13 inch baking dish with cooking spray or olive oil.
02 - Heat olive oil in a large skillet over medium heat. Add chopped onion and sauté for 3-4 minutes until translucent. Add minced garlic and cook for 1 additional minute until fragrant.
03 - Add ground beef to the skillet. Cook until completely browned, breaking up the meat with a wooden spoon as it cooks. Drain excess fat from the pan.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, dried basil, dried oregano, red pepper flakes, sugar, salt, and black pepper. Simmer uncovered over medium-low heat for 15-20 minutes, stirring occasionally to prevent sticking.
05 - Bring a large pot of salted water to a boil. Cook manicotti shells for 1-2 minutes less than package instructions. Drain and rinse gently with cold water to stop the cooking process and prevent sticking.
06 - In a large mixing bowl, combine ricotta cheese, 1½ cups mozzarella cheese, ¾ cup Parmesan cheese, egg, chopped parsley, ground nutmeg, salt, and black pepper. Mix until smooth and well combined.
07 - Fill each manicotti shell with the cheese mixture using a piping bag, spoon, or zip-top bag with the corner snipped off. Be gentle to avoid tearing the pasta shells.
08 - Spread 1 cup of meat sauce evenly over the bottom of the prepared baking dish. Arrange filled manicotti shells in a single layer over the sauce.
09 - Spoon the remaining meat sauce evenly over the manicotti, ensuring all pasta is covered. Sprinkle with 1 cup mozzarella cheese and ½ cup Parmesan cheese.
10 - Cover the baking dish tightly with aluminum foil. Bake for 25 minutes.
11 - Remove foil and continue baking for 10-15 minutes until the cheese is bubbly and golden brown on top.
12 - Let the manicotti rest for 10 minutes before serving to allow the filling to set. Garnish with fresh basil or parsley if desired.