01 - Preheat oven to 375°F. Lightly grease a 9×13 inch baking dish with cooking spray or a small amount of 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 browned, breaking up with a wooden spoon. 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 pepper. Simmer uncovered for 15-20 minutes, stirring occasionally until slightly thickened.
05 - Cook manicotti shells in salted boiling water for 1-2 minutes less than package instructions. Drain and rinse gently with cold water to stop the cooking process. Set aside on a clean towel.
06 - In a large mixing bowl, combine ricotta cheese, 1 1/2 cups mozzarella, 3/4 cup Parmesan, egg, parsley, nutmeg, salt, and pepper. Mix until smooth and fully incorporated.
07 - Transfer cheese mixture to a piping bag or zip-top bag with corner snipped off. Fill each manicotti shell with the cheese mixture, being careful not to overfill or split the pasta.
08 - Spread 1 cup of meat sauce evenly over the bottom of the prepared baking dish. Arrange filled manicotti in a single layer over the sauce.
09 - Spoon remaining meat sauce evenly over the manicotti. Sprinkle with 1 cup mozzarella and 1/2 cup Parmesan cheese.
10 - Cover baking dish tightly with aluminum foil. Bake for 25 minutes.
11 - Remove foil and continue baking for 10-15 minutes until cheese is bubbly and lightly golden brown.
12 - Let manicotti rest for 10 minutes before serving to allow filling to set. Garnish with fresh basil or parsley if desired.