Using a medium saucepan, combine the rice and water. Place over medium heat until water begins to boil. Cover pan and reduce it to lowest setting. Let simmer (covered) for 50 minutes. Remove from heat and let sit for 10 minutes covered. Fluff with a fork and set aside for later.

Using a medium saucepan, bring water to a boil. Add quinoa and return to a boil. Cover pan and reduce heat to medium. Let simmer (covered) for 12 minutes. Remove from heat, fluff with a fork, cover and let stand for 15 minutes. Set aside for later.

Preheat oven to 350°F. Spray a large baking dish with cooking spray; set aside.

Using a large bowl, combine the bread crumbs and milk. Let soak for 15 minutes.

Using a large skillet, add the sausage and onion; cook over medium-high until sausage is fully cooked.

Transfer cooked sausage and onions into bowl with breadcrumbs. Add cooked rice, cooked quinoa, egg, parsley, garlic, salt, pepper, oregano, basil, red pepper and Parmesan cheese. Mix until well combined.

Slice a thin layer off the top of each pepper. Remove seeds and inner membranes. Pour ~⅓ of tomato sauce into bottom of baking dish. Stuff peppers with the sausage and rice mixture. Place peppers upright in dish. Pour remaining tomato sauce over tops of peppers.

Cover dish tightly with foil and bake for 40-45 minutes, or until peppers are tender.

Remove foil. Sprinkle tops of peppers with shredded cheese. Bake for 5 more minutes, or until cheese has fully melted.

Before serving, spoon sauce from dish over peppers and garnish with additional chopped parsley.