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 finely chopped onion for 3-4 minutes until translucent. Add minced garlic and cook 1 minute more until fragrant.
03 - Add ground beef to the skillet. Cook until browned, breaking up with a wooden spoon as it cooks. Drain excess fat and return to heat.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, dried basil, dried oregano, red pepper flakes, sugar, salt, and black pepper. Simmer uncovered for 15-20 minutes, stirring occasionally until slightly thickened.
05 - Cook manicotti shells in salted boiling water 1-2 minutes less than package directions. Drain and rinse gently with cold water to stop cooking process. Set aside.
06 - Combine ricotta cheese, shredded mozzarella, grated Parmesan, egg, chopped parsley, ground nutmeg, salt, and black pepper in a large bowl. Mix until smooth and well 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 avoid tearing.
08 - Spread 1 cup of meat sauce evenly over bottom of prepared baking dish. Arrange filled manicotti in single layer over sauce.
09 - Spoon remaining meat sauce evenly over manicotti, covering completely. Sprinkle with remaining 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 10-15 minutes longer until cheese is bubbly and golden brown.
12 - Let manicotti rest 10 minutes before serving to allow filling to set. Garnish with fresh basil or parsley if desired.