Preheat oven to 400 degrees.
Cut off the top of 6 bell peppers about 1-inch down from top. Clean out seeds and membranes. Throw away the tops. Set aside.
In a large nonstick pan, brown ground beef, onions, and garlic. Be sure to break up ground beef into small pieces as it cooks. Stir often, until beef is browned. Pour beef into a colander and drain excess fat in the sink. Add back to pan. Stir in pasta sauce, tomatoes, Italian seasoning, pepper, and red pepper flakes. Mix well. Bring to boil, turn heat down to low and simmer for 5 minutes.
Stuff each bell pepper with about ¾ cup beef mixture. Stand peppers upright in ungreased baking dish. Pour 1 cup water in the bottom of the pan to steam the peppers, while baking.
Cover baking dish with foil and bake for 35 minutes. Remove foil. Sprinkle each with 2 teaspoons Parmesan cheese. Cook uncovered about 5 minutes more until cheese melts and peppers are soft.
These freeze great! Once cooled, wrap any leftovers well in plastic wrap and freeze.