Preheat oven to 375 degrees F.

Place a large cast iron or nonstick skillet over medium heat and add the olive oil. When the oil is shimmering, add the garlic, red pepper flakes, and onion, and cook for 2 to 3 minutes or until the onion is translucent. Add the tomatoes and their juices, season with salt and pepper and stir. Increase the heat to medium-high and bring to a boil, then lower to a simmer. After 5 minutes, add the basil. Continue to simmer the sauce for 5 minutes more or until it is thickened.

Make the filling. Combine the cheeses and egg in a large bowl. Season with salt and pepper.

Place a medium nonstick skillet over medium heat and coat with cooking spray. When some water flicked onto the skillet sizzles, add the spinach and toss until wilted, about 2 minutes. Remove from the heat and fold into the cheese mixture.

Assemble the manicotti. Reserve half of the sauce and spread the remaining evenly on the bottom of the skillet. Place the zucchini noodles on top, then add the remaining sauce. Create two wells in the noodles and add the cheese filling. Sprinkle the mozzarella over the skillet and season with pepper. Cover with foil and bake for 20 to 25 minutes or until the noodles have softened and the cheese is melted. Serve hot.