Preheat the oven to 350 degrees F. Pour ½ cup of marinara sauce in the bottom of a 9x9 inch baking dish (or a 9-inch round pie plate).
Cook the jumbo pasta shells according to the directions on the package.
In a large bowl, stir together the ricotta cheese, egg, all but ¼ cup of the Stella Aged Asiago, all but ¼ cup of the mozzarella, the basil, oregano, salt, pepper and pepper flakes.
Spoon the mixture into each shell. Place the shells in the baking dish on top of the marinara. Add the remaining marinara on top. Top with the remaining Stella Aged Asiago and mozzarella cheese. Top with the pepperoni.
Bake for 30 to 35 minutes, until golden and bubbly. Remove the shells from the oven and top with fresh basil and more asiago if you wish. Serve!