Bring a large pot of salted water to a boil and cook the pasta shells according to the package directions—just until al dente. Drain carefully and place the shells upside down on a clean towel so they don’t stick together or retain excess moisture. Slightly under-cooked shells work best since they’ll continue cooking in the oven.
While the shells cook, heat olive oil in a skillet over medium heat. Add chopped onion and cook until soft and golden. Stir in garlic and red pepper flakes and sauté another minute. Add ground meat and cook, breaking it apart until fully browned. Deglaze the pan with white wine and let it simmer briefly to absorb flavor. Drain off excess fat and let the mixture cool.
In a large bowl, combine ricotta, eggs, grated Parmesan, mozzarella, and chopped parsley. Stir until smooth. Once the meat mixture has cooled slightly, fold it into the cheese mixture. The filling should be thick, creamy, and easy to spoon into the shells.
Preheat the oven to 400°F (200°C). Spread a thin layer of tomato sauce over the bottom of your baking dish. Fill each cooked shell generously with the meat-cheese mixture and place them open-side-up in the sauce. Spoon more tomato sauce over the top, leaving a little filling visible for presentation. Cover the dish with parchment paper, then tightly with foil. Bake for about 25–30 minutes. Remove the foil and bake an additional 5 minutes until the cheese is slightly golden and bubbly.