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1. Preheat oven to 375 degrees F. In a large ovenproof skillet, heat 2 tablespoons olive oil over medium-high heat. Add onion and cook until beginning to soften, 3 minutes. Add garlic, chili powder, 11/2 teaspoons cumin, and 1 teaspoon oregano and cook, stirring constantly, until fragrant, 2 minutes.
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2. Add onion mixture, chipotle chili and adobo sauce, and tomatoes to a blender and blend until smooth. Season with salt and pepper.
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3. Heat remaining 3 tablespoons olive oil over medium-high heat in the skillet. Add peppers and cook until beginning to soften, 3 minutes. Add beans and remaining 11/2 teaspoons cumin and 2 teaspoons oregano and season with salt and pepper. Cook 3 minutes, then stir in cilantro. Transfer to a bowl.
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4. In same skillet, pour 1/2 cup sauce in bottom of skillet. Layer on 1/3 of the bean mixture, sprinkle with 1/3 of cheese, and layer with tortillas. (Tear tortillas to create an even layer.) Continue layering with sauce, bean mixture, cheese, and tortillas until skillet is full, ending with a layer of cheese.
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5. Bake until cheese is melting and sauce is bubbling, 15 minutes. Heat broiler and broil until top is nicely browned, 1 minute.
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6. Garnish with cilantro and serve.
