Preheat the oven to 375°F. Lightly grease a 9 x 13-inch baking dish.
Bring a large pot of salted water to a boil. Cook the jumbo pasta shells according to the package directions until just shy of al dente.
Drain the shells and rinse them under cool water to stop the cooking process. Set aside until cool enough to handle.
Heat the olive oil in a large skillet over medium heat. Add the ground beef and diced onion.
Cook, breaking the beef apart with a wooden spoon, until the meat is browned and the onion is tender. Drain any excess grease.
Stir in the garlic, Italian seasoning, salt, black pepper, and crushed red pepper flakes, if using. Cook for 1 minute, or until the garlic is fragrant.
Pour the marinara sauce into the skillet and stir until combined with the seasoned ground beef. Remove from the heat.
In a large mixing bowl, combine the ricotta cheese, egg, Parmesan cheese, and 1 cup shredded mozzarella cheese. Stir until evenly combined.
Prepare the baking dish. Spread about 1 cup of the meat sauce evenly across the bottom of the prepared baking dish.
Spoon the ricotta mixture into each cooked pasta shell. Arrange the filled shells in the baking dish with the open sides facing up.
Spoon the remaining meat sauce over and into the stuffed shells.
Sprinkle the remaining 1 cup shredded mozzarella cheese evenly over the top.
Cover the baking dish with aluminum foil and bake for 25 minutes.
Carefully remove the foil and bake for another 10 minutes, or until the sauce is bubbling and the mozzarella is completely melted.
Remove the stuffed shells from the oven and let them rest for about 5 minutes. Garnish with chopped fresh parsley, if desired, and serve warm.