Prepare the Pasta Shells:

1. Cook the Jumbo Shells: Bring a large pot of salted water to a boil. Add the jumbo pasta shells and cook according to the package directions, typically about 10-12 minutes. Make sure they are al dente (firm to the bite), as they will cook further in the oven. Drain and set aside to cool.
2. Drizzle with Olive Oil: Once the shells are drained, toss them with a little olive oil to prevent them from sticking together.

Prepare the Beef Filling:

3. Cook the Ground Beef: While the pasta is cooking, heat 1 tablespoon of olive oil in a large skillet over medium heat. Add the chopped onion and minced garlic and sauté for about 3-4 minutes, until the onion is soft and translucent.
4. Brown the Ground Beef: Add the ground beef to the skillet. Break it up with a wooden spoon and cook for about 8-10 minutes, or until the beef is browned and fully cooked through. Drain any excess fat if needed.
5. Season the Beef: Add the dried oregano, dried basil, red pepper flakes (if using), salt, and pepper to the beef. Stir well to combine. Taste the mixture and adjust the seasoning if necessary. Remove from heat and let the mixture cool for a few minutes.

Prepare the Cheese Mixture:

6. Mix the Cheeses: In a medium bowl, combine the ricotta cheese, 1 cup of shredded mozzarella, and ½ cup of grated Parmesan cheese. If you prefer a firmer filling, add 1 beaten egg to the cheese mixture. This will help bind the filling together. Stir until everything is well combined.

Stuff the Shells:

7. Stuff the Shells: Preheat your oven to 375°F (190°C). Take each cooked pasta shell and fill it with the beef mixture, then top it with a spoonful of the cheese mixture. Be generous with the filling to ensure each shell is packed with flavor. Arrange the stuffed shells in a single layer in a 9×13-inch baking dish.

Assemble the Dish:

8. Top with Marinara Sauce: Pour the marinara sauce evenly over the stuffed shells, covering them completely. Sprinkle the remaining shredded mozzarella cheese on top of the sauce, followed by the remaining Parmesan cheese.
9. Bake: Cover the baking dish with aluminum foil and bake for 25-30 minutes, until the cheese is melted and bubbly. For a golden, crispy top, remove the foil and bake for an additional 10 minutes.
10. Cool and Serve: Once the stuffed shells are done, remove the dish from the oven and let it cool for 5-10 minutes. Garnish with freshly chopped basil or parsley for added flavor and color.

Cut and Serve:

11. Slice into Portions: Using a sharp knife, cut the stuffed shells into squares, making sure each serving contains a few stuffed shells. Serve hot with a side of garlic bread or a green salad.