Saute onions, garlic and squash in butter over medium heat. Cook until tender and lightly browned, stirring as you go, about 6 minutes. Pour in chicken stock and reduce liquid by half. If desired, mash the squash and onions together using a potato masher to help dissolve into the sauce. Pour in cooked pasta and the cheeses little by little, stirring as you go. Pour in splashes of milk if needed to thin out melted cheese to create sauce. After all the cheese is melted into the pot, continue stirring and adding in milk. At first there may seem like a big wad of cheese melted in the middle, but as you keep stirring and adding in the milk bit by bit, it should come together to form a very cheesy sauce. Add nutmeg, salt and pepper to taste and serve hot.