Preheat oven to 425 degrees. Wash, peel, and cut butternut squash. Chop onion. Toss the butternut squash and onions with coconut oil and place onto a lined cookie sheet; bake for 15-20 minutes until slightly browned. While veggies are roasting, cook pasta according to package directions. Drain. Once veggies are done, remove from oven and allow to cool slightly. Add to a blender and puree. Mix together the macaroni, butternut squash puree, most of the cheddar cheese, and most of the parmesan. Once fully mixed, place into an oven-safe dish and top with remaining cheeses. Bake for 10 minutes, or until bubbly and slightly browned.