Preheat oven to 400F and lightly spray a baking sheet with non-stick spray.
Place each half of the squash cut side down, then pour in enough water to fill ½ inch of the pan. Bake in preheated oven until very fork tender, about 30-45 minutes (depending on size). Remove when done and let cool enough to handle.
While the squash is roasting, cook pasta shells according to directions, until al dente, and set aside.
Remove the cooked squash with a spoon and place into a bowl, then discard the skins. Add in the maple syrup, nutmeg and sea salt and mix thoroughly.
For the sauce, melt butter in a saucepan over medium heat.
Pour in the heavy cream, sage and garlic salt. Reduce heat and continue to cook the sauce (without boiling), until it has slightly thickened, about 3-4 minutes.
Gradually add in the ½ cup of parmesan cheese and stir until completely melted.
Pour enough sauce to make a thin layer on the bottom of a baking dish.
Spoon about 2 tablespoons of butternut filling into each shell, and place in the dish. Repeat until all shells are filled, then pour remaining sauce over top. Sprinkle with remaining parmesan cheese.
Cover with foil if desired and bake until sauce starts to bubble (about 10-15 minutes).