Cut the butternut squash in half and spoon out the seeds. Place on baking sheet cut-side down. Add some water and bake until a knife slides through the skin and the squash easily. Cool and then spoon the flesh from the shell. Set aside for later use.
Raise the oven temperature to 400 degrees F.
Place the ricotta, cream, garlic, shallots, basil, oregano and red paper flakes in a medium-size bowl. Whisk to combine until there are no lumps.
Mince up the sage and add to the ricotta mix. Adjust the seasoning with salt and pepper. Whisk until blended and set aside for later use.
Take 1 cup of the marinara and evenly coat bottom of each pan. Lay sheet of pasta. Spread some ricotta mixture on each and top with 3 cups spinach. Add another sheet pasta, ricotta and then ½ squash, masking layer pieces. Add another layer pasta. Top with marinara, ricotta, and 3 cups spinach on each.
Add last layer of pasta and pour remaining marinara over. Finish with parmesan and mozzarella. Wrap each in parchment then aluminum foil. Bake 1 to 1 ¼ hours. Let cool, then cut and serve.