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 minute more 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 pepper. Simmer uncovered over medium-low heat for 15-20 minutes, stirring occasionally to prevent sticking.
05 - Cook manicotti shells in a large pot of salted boiling water for 1-2 minutes less than package directions. Drain carefully and rinse gently with cold water to stop the cooking process. Set aside to cool slightly.
06 - In a large mixing bowl, combine ricotta cheese, 1½ cups mozzarella, ¾ cup Parmesan, egg, parsley, nutmeg, salt, and black pepper. Mix until smooth and thoroughly combined.
07 - Transfer cheese filling to a piping bag or zip-top bag with corner snipped. Pipe filling into each manicotti shell, filling from both ends if needed. Alternatively, use a small spoon to stuff the shells.
08 - Spread 1 cup of the meat sauce evenly over the bottom of the prepared baking dish. This prevents the pasta from sticking and ensures even cooking.
09 - Place filled manicotti shells in a single layer over the sauce, leaving a small space between each piece. Arrange them in the same direction for easier serving.
10 - Spoon the remaining meat sauce evenly over the manicotti, covering completely. Sprinkle with the remaining 1 cup mozzarella and ½ cup Parmesan cheese.
11 - Cover the baking dish tightly with aluminum foil. Bake for 25 minutes to allow the pasta to cook through and flavors to meld.
12 - Remove foil and continue baking for 10-15 minutes more until the cheese is bubbly and lightly golden brown on top.
13 - Let the manicotti rest for 10 minutes before serving. This allows the cheese filling to set slightly, making it easier to serve. Garnish with fresh basil or parsley if desired.