Preheat your oven to 375°F and position the rack in the upper third of the oven. Bring a large pot of salted water to a boil and cook the pasta for 2 minutes less than the time indicated on the package. Once cooked, drain the pasta and transfer it to a 9×13-inch baking dish. Meanwhile, heat a skillet over medium-high heat and add the sausage and chopped onion. Cook, stirring occasionally, until the sausage is browned, about 8–10 minutes. If there’s excess fat, carefully spoon most of it out. Stir in the minced garlic and cook for about one minute. Add the marinara sauce and crushed red pepper flakes, then cook for a few more minutes until heated through. Pour the sausage sauce mixture over the pasta in the baking dish, season with salt and pepper to taste, and toss until everything is well coated. Spread the mixture evenly in the dish. Sprinkle the shredded mozzarella or cheddar and grated Parmesan cheese evenly on top. Bake uncovered for 15 minutes, then switch to broil for a few minutes to brown the cheese—keep a close eye to avoid burning. Serve immediately.