Heat the oven to 375°F and grease a 9-by-13-inch dish. Warm the tortillas wrapped in a damp towel in the microwave until flexible.
Brown the beef and onion and drain. Stir in cumin, chili powder, salt, beans, tomatoes and 1 cup enchilada sauce.
Spread 1/2 cup sauce in the dish. Layer four tortillas, half the beef mixture and 1 cup cheese. Repeat.
Top with the remaining tortillas, sauce and cheese. Cover with foil.
Bake 25 minutes, uncover and bake 8 to 10 minutes more. Rest 15 minutes before cutting.