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 the finely chopped onion for 3-4 minutes until translucent and softened. Add minced garlic and cook for 1 additional minute until fragrant, being careful not to burn it.
03 - Add ground beef to the skillet and cook until thoroughly browned, breaking up the meat with a wooden spoon as it cooks. Drain excess fat from the skillet before proceeding.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, dried basil, dried oregano, red pepper flakes (if using), sugar, salt, and black pepper. Reduce heat to low and simmer uncovered for 15-20 minutes, stirring occasionally to prevent sticking, until sauce thickens slightly.
05 - Bring a large pot of salted water to a boil. Cook manicotti shells for 1-2 minutes less than package instructions (they will finish cooking in the oven). Drain carefully and rinse gently with cold water to stop the cooking process and prevent sticking.
06 - In a large mixing bowl, combine ricotta cheese, shredded mozzarella, grated Parmesan, egg, chopped parsley, ground nutmeg, salt, and black pepper. Mix until completely smooth and well incorporated.
07 - Fill each manicotti shell with the cheese mixture using a piping bag, a small spoon, or a zip-top bag with the corner snipped off. Be careful not to overfill or split the pasta tubes.
08 - Spread 1 cup of the meat sauce evenly over the bottom of the prepared baking dish. Arrange filled manicotti shells in a single layer over the sauce, leaving slight space between each piece.
09 - Spoon the remaining meat sauce evenly over the manicotti, covering completely. Sprinkle with the remaining mozzarella and Parmesan cheese.
10 - Cover the baking dish tightly with aluminum foil and bake for 25 minutes. The foil helps steam the pasta and prevents the cheese from browning too quickly.
11 - Remove the foil and continue baking for 10-15 minutes longer, until the cheese is bubbly and golden brown on top.
12 - Let the manicotti rest for 10 minutes before serving to allow the filling to set. Garnish with fresh basil or parsley if desired.