Spray a large skillet with nonstick spray; saute onions and peppers over medium-high heat.
When the vegetables are tender, add the cumin, chili powder and the can of chopped tomatoes; simmer in the skillet for 5-10 minutes.
In a large bowl, mix together black beans, pinto beans and chiles; mix in jar of salsa.
Spray the bottom a 9"x13" baking dishes with cooking spray.
Place two tortillas on the bottom of the dish. Spread one-third of the vegetable mixture onto the tortillas, then one-third of the bean mixture; then sprinkle one-third of the cheese on top. Repeat layering two more times, finishing with the cheese.
Cover with foil and bake for 25 minutes; uncover and bake an additional 10 minutes.
Remove from oven and let stand five minutes before cutting and serving.
Serve with fresh cilantro and a dollop of light sour cream, if desired.