Preheat oven to 400 degrees.
Cut tops of acorn squash off. Scoop out seeds and pulp leaving about 1-2 inches on the sides and bottom. Place acorn squashes on baking sheet.
Melt butter in microwave then use a basting brush to spread butter on top and inside of each acorn squash.
Bake squash for 40-50 minutes, until tender with a fork.
Meanwhile, cook pasta according to directions on box then use a colander to strain it.
Melt butter in the same pot on medium/low heat. Add in the flour, salt, and pepper, and stir until combined to make a roux.
Gradually add in milk while stirring until sauce starts to thicken, 3-4 minutes.
Remove pot from heat and immediately add in cheddar cheese. Stir until melted.
Pour pasta into cheese mixture and mix well to combine.
Serve immediately or refrigerate for up to 5 days. Reheat prior to eating.