Parboil peppers; half-fill lg saucepan with cold water. Bring to boil over high heat. Using a paring knife, trim the top 1/2 inch off of the peppers, remove seeds & ribs. For peppers to stand, trim about 1/4 inch off of the bottoms, be careful not to cut through to the bottoms. Simmer the peppers in the water, uncovered for 3 min. Remove with tongs and drain.
To make sauce: in med-sized saucepan, bring tomatoes, water and basil to boil over med-high heat. Set aside. Preheat oven to 350°F. Spray a 8-inch round baking pan with cooking spray.
To make stuffing: In small skillet heat oil over med-high heat. Add onion & garlic, saute for 5 min or until soft. Remove skillet from heat. Set aside. Stir in rice, half the tomato sauce, parsley, marjoram, salt, red pepper flakes and cheese. Stuff the rice mix into peppers equally. Stand them upright in the baking pan.
Bake uncovered for 30 min. Top the peppers with the remaining tomato sauce, continue baking 10 min or until peppers are tender and sauce is bubbly.