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 to a skillet, along with the onion. 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. Spoon out excess fat from the pan.
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.
Spread the cheese layer evenly over the pasta/sauce layer. This step can get a little messy. It doesn't have to be done perfectly.
Add the remaining pasta/sauce mixture and spread it out evenly, then top the casserole with the mozzarella cheese.
Cover the casserole dish with foil and bake for 30 minutes, then remove the foil and broil for a few minutes (watch it carefully) until the cheese is bubbly and browned.
Let the casserole sit for 5-10 minutes, then use a spatula to cut it into individual portions. Season with salt & pepper if needed. Note: Especially when it's still hot, you won't get nice, even squares with a perfectly even cheese layer. It'll mix together a bit, but I went for plenty of sauce (especially so leftovers aren't dry).