Preheat your oven to 375F and move the rack to the top third of the oven.
Boil a large, salted pot of water for the pasta. Cook it 2 minutes less than package directions indicate. Once it's done, drain it and add it back to the pot it was cooked in and set aside.
Meanwhile, take the sausage meat out of its casings and add it, along with the onion, to a skillet over medium-high heat. Cook it for about 10 minutes, breaking it up with your spoon as you go along and stirring occasionally, until it's cooked.
To the skillet, stir in the garlic and red pepper flakes, then continue cooking it for another minute or so. Spoon out most of the excess fat.
To the skillet, stir in the marinara sauce and warm it through for a few minutes.
To the pot with the pasta, add in about 1/2 of the skillet sausage/sauce mixture and give it a stir. Transfer it to a 9x13 baking/casserole dish and spread it in an even layer.
Add the ricotta (I just use a spoon to dollop it on) to the pasta, and then sprinkle the parmesan over top.
Spoon the rest of the sausage/meat mixture over top the pasta.
Add the cheddar and mozza in an even layer over top the pasta.
Bake, uncovered, for 20 minutes, and then broil for a few minutes to brown the cheese (watch it carefully). Let sit for about 5 minutes prior to serving, then enjoy!