Preheat oven to 425°F. Lightly grease baking pan or pans and keep ready.

Cook pasta according to package instructions until al dente. Drain and set aside.

Heat 1tbsp oil in a pan, add the onions and cook on medium flame, stirring occasionally until the onions are nicely caramelized. Season with salt and pepper, remove and set aside.

Squeeze all the water from the thawed spinach and keep ready.

In a medium sauce pan, melt butter and whisk in flour. Cook on medium flame until the flour changes color and doesn't smell raw anymore.

Slowly stir in the warm milk and whisk to form a lump free mixture. Add red pepper flakes, dried basil, oregano, salt and pepper. Cook till the mixture thickens a little bit. Add the thawed spinach and mix to combined. Stir in the grated provolone, parmesan and half of the mozzarella cheese. Whisk until the cheese melts. Turn off the heat.

Add the cheese sauce, most of the caramelized onions (reserve some for the topping) to the pasta and mix well.

Pour into the prepared pan and top with the remaining caramelized onions and the remaining parmesan cheese. Bake for 20~25 minutes or until the top is bubbly and browned. Let rest for a few minutes before serving.