Preheat oven to 400˚ F. Slice butternut squash in half and scoop out seeds. Place each half cut side down in a 9x13 pan and pour 1/2" of water in the bottom. Place in oven and bake until tender, about 30 to 45 minutes. Once done, remove and set aside.
Rinse quinoa and set aside. In a medium pan heat olive oil over medium low heat. Dice shallots, add to oil, and saute until shallots are fragrant. Stir in quinoa and water. Bring to a boil, reduce to a simmer, and let cook until water is absorbed, 12-15 minutes.
While quinoa cooks, scoop out butternut squash leaving a 1/4" to 1/2" on the sides and bottom. Drain water from pan and return butternut squash to the pan, cut side up.
Mash butternut squash and stir in gorgonzola cheese. Once quinoa is done, add it to the butternut squash along with the salt, pepper, and any herbs you might like to use.
Scoop filling evenly into butternut squash halves. Sprinkle with extra gorgonzola cheese and return to oven. Let bake for 10-15 minutes or until cheese has melted and the tops begin to brown. Remove from oven, cut eat half in half, and serve.