Preheat oven to 350 degrees F. Cut your squash lengthwise in half and using a spoon scoop out the seeds. Place the pieces skin side down on a baking sheet and roast for 1 hour. When cool to the touch, scoop out 1 cup and add to a blender.
Add all other ingredients to the blender with the butternut squash and blend on high for about 30 seconds or until creamy. Taste and add more salt/pepper to your liking.
Bring a pot of salted water to boil. Cook pasta al dente according to box instructions (about 9 minutes). Drain and wash with cold water to stop it from cooking and is cool to the touch.
In a baking dish (I used a cast iron skillet), line the bottom with about 1/3 cup of the cheese sauce. Place the pasta shells in your dish. Fill each shell with the cheese sauce. Top with shredded cheese and everything bagel seasoning.