Heat your oven to 400°F. Rub the cut sides of the squash with 1 tablespoon of your olive oil and season with salt and pepper. Place cut side down on a baking sheet and roast for 30 to 40 minutes, until fork-tender and browned at the edges.
Cool a few minutes, then scoop out the flesh and blend until you get a pure. Lave the oven on.
While the squash roasts, bring a large pot of water to a boil. Once boiling, season with kosher salt. Cook the shells 2 to 3 minutes less than the package directions. Drain and set aside.
In a large pot, melt your butter over medium heat. Whisk in the flour and cook 1 to 2 minutes. Add a pinch of nutmeg and season with salt and pepper
Sowly whisk in the beer, then the milk. Simmer gently, whisking often, until the sauce coats the back of a spoon, about 5 minutes. Stir the puree into the cheese sauce.
Remove the pot from the heat. Reserve about 1 to 1.5 cups of your shredded cheese. Stir in the Manchego and cheddaraa handful at a time until melted and smooth. Season with salt and pepper.
Add in your pasta, tossing to combine.
Transfer your mac and cheese to a baking dish and top with your cheese you set aside. Bake in the oven for 10 to 15 minutes, until bubbly and golden. Rest and scoop to enjoy!
Notes
Remove the pot from the heat before the cheese goes in: If you put the cheeses in with the heat on, this will make the sauce grainy and oily.
Grate your own cheese: It melts more smoothly and creates a creamier sauce without any graininess.
Undercook your pasta: It will continue cooking in the oven!
Prep: You can prepare this ahead of time and warm it back up in the oven at the time of serving.
Storing: Store in an airtight container in the refrigerator for up to 3 days.