1. Preheat oven to 375°F. Cut squash in half lengthwise; remove seeds. Place in roasting pan and drizzle with olive oil. Place in oven and cook until soft all the way through, about 1 hour. Set aside until cool. When cooled, remove skin and place in food processor. Purée until smooth.
2. Melt butter in saucepan. Add flour. Stir to make a roux and cook 3 minutes, stirring the entire time. Add 3 cups milk and stir until thickened. Add the rest of the milk and bring to a boil, stirring occasionally. Add shredded cheese and stir until melted. Season with salt and pepper.
3. To assemble the dish: Place cooked elbow macaroni in bowl. Pour half of the cheese sauce over and add puréed, roasted butternut squash. Fold together. If it seems too dry, add the rest of the cheese sauce. Place in an ovenproof dish and heat for 15 minutes at 325 degrees.