Cook the penne pasta in salted water per the package instructions. Drain well then add back to the pasta pot.
Preheat oven to 350°F. Spray a 13x9 inch baking dish with cooking spray. Set aside.
Season chicken cubes on all sides using salt and black pepper. Drizzle a large skillet with olive oil over medium high heat. Add chicken and cook for 3-5 minutes or until browned and cooked through. Remove from skillet using a slotted spoon.
To the skillet add diced onion and crushed red pepper flakes. Continue to cook over medium high heat for 3 minutes or just until softened scraping any brown bits from bottom of pan. Add garlic cooking for 1 minute longer. Remove from heat.
Combine: To the cooked penne pasta add cooked chicken, onion, Italian seasoning, 5 cups marinara sauce and 2 cups mozzarella cheese. Mix to combine then pour into the baking dish.
Drizzle the top with the reserved 1 cup marinara and sprinkle with 1 cup mozzarella cheese.
Topping: In a small bowl, mix together panko breadcrumbs, Parmesan cheese and granulated garlic with melted butter. Sprinkle over shredded cheese.
Bake for 35-40 minutes or until bubbly and the top is golden.