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 3-4 minutes until translucent. Add minced garlic and cook 1 minute more until fragrant.
03 - Add ground beef to the skillet. Cook until completely browned, breaking up with a wooden spoon. Drain excess fat from the pan.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, basil, oregano, red pepper flakes, sugar, salt, and pepper. Simmer uncovered for 15-20 minutes over medium-low heat, stirring occasionally.
05 - Bring a large pot of salted water to boil. Cook manicotti shells 1-2 minutes less than package directions. Drain and rinse gently with cold water to stop cooking.
06 - Combine ricotta, 1½ cups mozzarella, ¾ cup Parmesan, egg, parsley, nutmeg, salt, and pepper in a large bowl. Mix until smooth and well blended.
07 - Transfer cheese mixture to a piping bag or zip-top bag with corner snipped off. Pipe filling into each manicotti shell, filling completely.
08 - Spread 1 cup meat sauce over bottom of prepared baking dish. Arrange filled manicotti in single layer over sauce.
09 - Spoon remaining meat sauce evenly over manicotti. 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 10-15 minutes until cheese is bubbly and golden brown.
12 - Let manicotti rest 10 minutes before serving. Garnish with fresh basil or parsley if desired.