Preheat your oven to 375F and move the rack to the top third of the oven.
In a medium bowl, add the cheese layer ingredients and stir them together until you've got a nice, smooth mixture. Set aside.
Boil a large, salted pot of water for the pasta and cook it 2 minutes less than package directions suggest. Once it's done, drain it and add it back to the same pot it was cooked in.
Meanwhile, add the sausage meat and onion to a skillet. Cook over medium-high heat, breaking the meat up as you go along, for about 10 minutes or until browned and cooked through.
To the skillet, stir in the garlic and red pepper flakes and cook for about a minute. Drain the excess fat.
Add the skillet mixture to the pot that has the pasta in it, and then pour in the marinara sauce. Toss until everything is coated (this is easiest to do with tongs or two large spoons).
Add half the pasta/sauce mixture to a 9x13 baking dish, then spread it in an even layer.
Spoon the ricotta over the pasta for the cheesy middle layer (you don't need to be too exact… I just put dollops here and there).
Add the remaining pasta/sauce mixture and spread it out evenly, then top with the mozzarella cheese.
Bake, uncovered, for 20 minutes, then broil for a few minutes (watch it carefully) until the cheese is bubbly and browned.
Season with salt & pepper if needed, and serve with some fresh basil and/or parsley if desired.