ROASTING BUTTERNUT SQUASH: Preheat oven to 375 degrees. Cut the butternut squash in half, lengthwise. Using a spoon, scoop out the stringy part and the seeds and discard.
Place the butternut squash, skin side down, onto a baking sheet. Sprinkle with 1/4 teaspoon salt and 1/4 teaspoon pepper, and drizzle with 1 tablespoon olive oil. Place in the oven and roast for 20 minutes.
While the squash is roasting, boil water in a large stock pot. Once water is boiling, add pasta and cook for about 10-15, or until it is al dente. Reserve about 2 cups of the cooking water and set it to the side. Drain and rinse pasta with cool water to stop the cooking process.
Melt 1 tablespoon of butter in a saucepan over medium-low heat. Add the diced onions and cook until they are translucent. When the onions are translucent, add 4 more tablespoons of butter to the saucepan to melt. Once melted, begin sprinkling in the flour a little bit at a time.
Whisk the flour into the butter into all of the butter is absorbed, it should have a creamy texture- along with the texture of onion. Slowly whisk in the milk or cream. If the mixture becomes too thick, add in a little bit of the reserved cooking water.
BUTTERNUT SQUASH PUREE: Scoop the cooled squash out of the shell with a spoon, and add it to a blender. Add 2-3 tablespoons of the reserved cooking water as well. Blend on high for 1 minute until a semi-thick puree is formed. Pour the butternut squash puree into the milk mixture.
Start to add in the cheese, a little bit at a time. Mix well using a sturdy spoon. Once all of the cheeses are added, add all of the seasonings and mix them in well. Remove cheese mixture from the heat.
Reduce the oven to 350 degrees. Lightly spray and 9x11 baking dish with non-stick cooking spray. Pour your pasta shells into the baking dish, and add the crab meat. Combine the crab meat with the pasta until evenly distributed.
Pour the cheese sauce over the pasta and crab, and combine well. Bake uncovered for 15 minutes.
Remove from the oven and let it rest for 10 minutes, and sauce will continue to thicken.