1. Preheat your oven to 375°F. Lightly grease a 9×13-inch baking dish to prevent sticking.
2. Bring a large pot of salted water to a boil. Add the jumbo pasta shells and cook according to package instructions until al dente—usually about 8 to 10 minutes. Drain and rinse with cold water to stop the cooking. Set aside on a lightly oiled sheet to prevent sticking.
3. In a large skillet over medium heat, sauté the diced onion and minced garlic in a tablespoon of olive oil until soft and fragrant, about 3-4 minutes.
4. Add the ground beef to the skillet. Break it apart with a wooden spoon and cook until browned and cooked through, about 6-8 minutes. Drain excess fat if necessary.
5. Season the beef mixture with salt, black pepper, Italian seasoning, and crushed red pepper flakes if using. Stir well to combine and then remove from heat to cool slightly.
6. In a large mixing bowl, combine the ricotta cheese, half of the mozzarella, half of the Parmesan, and the egg. Add the cooled beef mixture and mix gently until all ingredients are well incorporated. Taste and adjust seasoning if needed.
7. Spoon about 1 to 2 tablespoons of marinara sauce evenly on the bottom of your prepared baking dish.
8. Carefully stuff each cooked shell with the beef and ricotta mixture and place them in the baking dish, open side up, nestled close together.
9. Pour the remaining marinara sauce evenly over the stuffed shells, then sprinkle with the remaining mozzarella and Parmesan cheese.
10. Cover the dish with foil and bake in the preheated oven for 25 minutes. Remove the foil and bake for an additional 10 minutes, or until the cheese is bubbly and golden.
11. Remove from oven and let rest for 5 minutes before serving. Garnish with fresh basil or parsley for a pop of color and flavor.

One of my favorite tips from years of making this dish is to let it rest a bit after baking. It helps the filling set and makes serving easier. Plus, it gives you a moment to catch your breath and soak in the wonderful aromas filling your kitchen.