Preparation

1. Preheat an oven to 400°F.
2. Line a baking pan with foil. Add the squash, olive oil, a pinch of the salt, the pepper, thyme, and sage onto the pan and toss to combine. Once the oven is preheated, add the pan and roast the squash until they are starting to caramelize and soften. 
3. While the squash is cooking, put the crackers into the work bowl of a food processor fitted with the chopping blade. Process until finely chopped. Remove and reserve.
4. With the chopping blade still in the food processor, add the cooked squash to the work bowl. Pulse a few times, and then process until smooth. Scrape down the bowl and then add the cream cheese, remaining salt, and spices. Pulse a few times, and then process until smooth. Reserve.
5. In a large pot or casserole, cook the pasta until al dente. Drain and then return to the cooking pot. Add the milk and the reserved cream cheese-squash mixture, stirring until well combined.
6. Remove the chopping blade from the work bowl and then fit with the medium shredding disc (no need to clean the bowl). Shred the cheeses, and then stir into the pasta mixture.
7. Transfer the pasta mixture to the pot. Top with the reserved cracker crumbs.
8. Reduce the oven temperature to 375°F. Transfer the macaroni and cheese into the oven and cook until the mixture is bubbling and top is lightly browned.
9. Cool slightly before serving.