Preheat the oven to 375°F (190°C). Spread 1/2 cup of marinara sauce in the bottom of a 9 x 13 inch baking dish and set aside.

Bring a large pot of salted water to a boil. Add the manicotti and cook 2 minutes less than package directions, about 6–7 minutes. Drain and rinse gently under cool water.

While the pasta cooks, heat olive oil in a large skillet over medium-high heat. Add ground beef and cook 5–7 minutes, breaking it up, until browned.

Stir in diced onion and minced garlic; cook 2–3 minutes until the onion softens. Remove from heat and let the mixture cool for 5 minutes.

In a medium bowl combine ricotta, 1 cup mozzarella, Parmesan, egg, salt, pepper, Italian seasoning and red pepper flakes. Mix gently until just combined.

Fold the cooled beef mixture into the ricotta mixture until evenly distributed.

Using a small spoon, fill each manicotti tube about three-quarters full with the meat and cheese filling.

Arrange the stuffed manicotti seam-side up in the prepared baking dish in a single layer.

Pour the remaining marinara sauce evenly over the pasta, making sure all tubes are coated. Sprinkle the remaining 1/2 cup mozzarella over the top.

Cover the dish tightly with aluminum foil and bake for 35 minutes. Remove the foil and bake an additional 10–12 minutes until the cheese is golden and the sauce is bubbly. Let rest 5 minutes before serving.