Sprinkle in flour and then stir continuously until it has a paste like texture.
Slowly pour in milk while stirring continuously and it has a smooth, creamy texture.
Add in the pureed butternut squash and continue stirring until there are no more lumps, and the butternut squash puree has blended in smoothly with the creamy sauce.
Slowly sprinkle in both the sharp cheddar and chipotle Monterey jack shredded cheeses. Continue stirring until the cheese melts.
Add in the cooked macaroni and stir until the macaroni is completely covered in sauce and heated through.