Heat oven to 375° F. Spread 1 cup of the salsa in a 9-by-13-inch baking dish and top with 6 tortillas. Top with 1 more cup of the salsa, a third of the butternut squash, a third of the beans, and 1 cup of the cheese, spreading evenly. Repeat the layering 2 more times, reserving the final 1 cup of cheese. Cover with foil.
Bake for 1 hour, until the squash is tender. Uncover and sprinkle with the reserved 1 cup of cheese. Broil 8 inches from the heat for 2 to 3 minutes, until bubbling and browned in spots. Remove from oven and let stand for 15 minutes. Top with dollops of sour cream and top with the cilantro and jalapeños before serving.