Preheat oven to 375F and move the rack to the top third of the oven.
Boil a salted pot of water for the pasta. Cook it for 2 minutes less than the package directions indicate. Once it's done, drain it and set it aside.
Crumble the sausage meat directly into a skillet, and add the onion in too. There should be enough fat released by the sausage to cook the onion, but if it's particularly lean, add a tablespoon of olive oil. Cook over medium-high heat, stirring occasionally, until the sausage has browned (about 10 minutes). If there's a lot of excess fat, spoon most of it out.
Stir in the garlic and cook for about a minute.
Add in the marinara sauce and red pepper flakes and cook for a couple more minutes until it's warmed through.
Add the drained pasta to a 9x13 baking dish and then pour the sausage mixture over top. I add in some salt & pepper as well. Toss until everything is coated. Smooth it out into an even layer.
Top with the cheeses and bake, uncovered, for 15 minutes. Broil for a few minutes to brown the cheese (watch it carefully). Serve immediately.