In a medium bowl, add cooked onions, pizza sauce, pepperoni, Italian seasonings, red pepper flakes, and ½ cup mozzarella cheese. Mix well. Divide sauce and stuff each bell pepper. Top each stuffed pepper with 2 tablespoons shredded mozzarella cheese. Next, sprinkle each with 1 teaspoon Parmesan cheese. Place each in a 9-inch baking dish. Pour 1 cup water in the bottom of baking dish. Loosely cover the dish with foil so it doesn’t stick to top as cheese begins to melt. Bake for 40 minutes. Remove foil and bake additional 5 minutes, uncovered. If peppers are not soft enough, cook about 5 minutes more.