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.
This is FANTASTIC and easy! Makes a lot so be prepared to have leftovers.