Slice the tops off of the peppers and clean the seeds out. Take the tops you just cut of the peppers and dice as much of the pepper from it as you can and use it in the filling.
Place the 4 peppers in an 8 x8 ( or 9x9) pan upright. If necessary cut a little off the bottom of the pepper to make it stand upright.
Brown the ground beef in a saute pan. Remove the ground beef from the pan and wipe the pan out. Add 2 Tablespoons olive oil to the pan. Saute chopped peppers(from the tops of the peppers) , diced onions and half the can of drained diced tomatoes. Season the mixture with salt, pepper and garlic powder. Saute for about 10 minutes or until peppers are tender. Add the cooked rice, cooked ground beef, 1/2 cup mozzarella and 1/2 cup cheddar to the pan. Stir to combine well. Stuff each pepper with the meat mixture. Pour remaining diced tomatoes over the stuffed peppers, add the red pepper flakes to the juice from the tomatoes on the bottom of the pan.
Cover with foil, bake at 350 degrees for 1 hour. Remove the foil from the pan and top each pepper with a combination of the mozzarella and cheddar cheeses (1/2 cup each) bake another 15 minutes and serve.