Melt butter in a large pan over medium-high heat. Slowly whisk in flour.
Cook over medium-high heat for 1-2 minutes, until lightly brown.
Whisk in the milk slowly, mixing to ensure there are no clumps (3-4 minutes).
Add 1/2c grated cheese slowly, mixing to ensure absorbed.
Reduce heat to simmer. Season lightly with pepper.
Simmer 4-5 minutes, or until sauce begins to thicken. Remove from heat.
Using a slotted spoon, add in the tender butternut squash.
Mix squash into sauce.
Once combined, add in cinnamon and 1/2 chopped sage. Season with salt and pepper to taste.
Add in reserved water and pasta.
Transfer into a 8x10 baking dish.
Top with remaining sage and cheese.
Bake for 5-7 minutes, or until cheese is melted.