Preheat oven to 375 degrees. Cut butternut squash in half, lengthwise, and scoop out seeds. Place in baking dish, flesh side down, and pour water in the baking dish. Roast in oven for 35-40 minutes, until soft. Scoop out cooked flesh and discard skin. Set squash flesh aside.
Cook pasta according to package directions, omitting salt. Drain and set aside.
Meanwhile, place butternut squash, Greek yogurt, milk, chicken broth, salt, black pepper, nutmeg and cayenne in a blender and puree until smooth. (If squash is still hot, remove plastic cap from blender lid and place a kitchen towel over it so steam can escape and the hot contents don’t explode.)
Heat butter in a saucepan and add squash puree. Add marble jack, Gruyere and half of the Parmesan cheese and cook on medium, stirring, until cheese is melted. Taste and adjust seasoning, if necessary.
Coat a 13×9 baking dish with cooking spray. Add cooked pasta to the baking dish and pour in the squash/cheese sauce. Stir until combined. Place in oven and bake for 20 minutes.
Remove dish and turn oven on low broil. Top pasta with remaining Parmesan cheese and bread crumbs. Spray top with cooking spray. Place back in the oven and broil for 4-5 minutes, until top is browned, rotating the dish if necessary.
Remove from the oven and sprinkle with parsley.
*You can cook the squash up to 3 days in advance. You can also use 2 10 ounce bags of frozen cubed squash; thaw and place into the blender and puree with the other sauce ingredients.