Preheat oven to 375 degrees F (190 degrees C).
Place squash on a baking sheet, and bake 40 minutes, or until tender. Remove from heat, cool, and shred pulp with a fork.
Reduce oven temperature to 350 degrees F (175 degrees C). Lightly grease a casserole dish.
In a skillet over medium heat, cook the ground beef until evenly brown. Drain, and mix in the green pepper, red pepper, red onion, and garlic. Continue to cook and stir until vegetables are tender.
Mix the shredded squash and tomatoes into the skillet, and season with oregano, basil, salt, and pepper. Cook and stir until heated through. Remove skillet from heat, and mix in 2 cups cheese until melted. Transfer to the prepared casserole dish.
Bake 25 minutes in the preheated oven. Sprinkle with remaining cheese, and continue baking 5 minutes, until cheese is melted.