Preheat oven to 400°F. Oil a large (9x13”) baking dish.
Halve the peppers and clean out the seeds and membranes. Rub a little olive oil on the inside of each pepper. Place in baking dish and sprinkle with salt and pepper. Roast for 15 minutes, until peppers are soft but undercooked. Remove from oven and set aside.
Meanwhile, heat a large skillet over medium heat. Add the remaining olive oil and saute the onion until soft, about 3 minutes. Add in the ground beef and cook until no longer pink. Drain off any fat if necessary.
Stir in garlic and cook until fragrant, about one minute. Stir in the tomato sauce, Italian seasoning, salt and pepper to taste. Sprinkle with red pepper flakes. Cook for about 2 minutes more.
Spoon this mixture into the peppers. Top each one with shredded mozzarella and cover with a slice of colby jack cheese.
Lower oven temperature to 350°F and bake for 20 to 25 minutes, until cheese is melted and pepper is soft and tender, and edges are starting to brown.
Remove from oven and allow to cool for 5 minutes. Serve warm.