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. Sauté chopped onion 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 browned, breaking up meat with a wooden spoon. Drain excess fat and set aside.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, dried basil, dried oregano, red pepper flakes, sugar, salt, and pepper. Simmer uncovered for 15-20 minutes, stirring occasionally until slightly thickened.
05 - Boil manicotti shells in salted water for 1-2 minutes less than package instructions. Drain and rinse gently with cold water to stop cooking process.
06 - Combine ricotta cheese, 1½ cups mozzarella, ¾ cup Parmesan, egg, parsley, nutmeg, salt, and pepper in a large bowl. Mix until smooth and fully incorporated.
07 - Fill each manicotti shell with cheese mixture using a piping bag, spoon, or zip-top bag with corner snipped off. Handle shells gently to prevent tearing.
08 - Spread 1 cup of meat sauce evenly across the bottom of the prepared baking dish. Arrange filled manicotti shells in a single layer over sauce.
09 - Spoon remaining meat sauce over pasta shells, ensuring even coverage. Sprinkle with 1 cup mozzarella and ½ cup Parmesan cheese.
10 - Cover baking dish tightly with aluminum foil. Bake at 375°F for 25 minutes.
11 - Remove foil and continue baking for 10-15 minutes until cheese is bubbly and golden brown on top.
12 - Allow manicotti to rest for 10 minutes before serving. Garnish with fresh basil or parsley if desired.