Preheat the oven to 350 degrees F. Spray a baking dish (I used a 9x9 but you can also do a 9x13, this should make enough shells and filling) with nonstick spray.
Heat a large skillet over low heat and melt the butter. Once melted, stir in the onions, squash and a pinch of salt and cook, stirring often, until the onions are caramely and golden, about 25 to 30 minutes. Add in the mushrooms and cook until they are soft and juice, about 6 minutes. Stir in the spinach and garlic, cooking until the spinach wilts.
In a bowl, stir together the ricotta and almost all of the fontina, reserving some for the top. Stir in the beaten egg. Add in the salt and pepper. Fold in the cooked vegetables until combined.
Spoon 1/2 cup of marinara in the bottom of the baking dish. Take the cooked pasta shells and fill them with the cheesy vegetable mixture and place them in the baking dish. Cover them with all of the marinara and the remaining fontina cheese. Bake for 30 to 35 minutes, until golden and bubbly.
Top with fresh oregano and basil to serve.