Add a tablespoon of olive oil to a skillet over medium-high heat. Once the oil begins to shimmer, add the onion, bell peppers, jalapenos, garlic, salt, and pepper. Cook, stirring occasionally, until golden brown and caramelized, about 15 minutes. Set aside to cool
Place 4 chicken breasts in a bowl near a wide work surface.
Combine the salt, pepper, paprika, oregano, cumin, garlic powder in a small bowl, and mix together with a fork.
Pour half of the spice mixture onto the chicken, set the other half aside to use later.
Rub all the spices onto the chicken until completely coated.
To pound out the chicken, first take a chicken breast and butterfly it by slicing half way into it to open it like a book, making sure not to slice it all the way through. Cover the breast with parchment paper or plastic wrap. Gently pound the meat with a mallet or rolling pin until it is evenly flattened, about ¼ inch (6 mm) in thickness.
Onto each pounded chicken breast, rub on about 2 tablespoons refried beans, 1 tablespoon chopped tomatoes, 1 tablespoon cotija cheese, and 1 tablespoon cooked black beans. Make sure to not overfill the pounded chicken.
Carefully roll the chicken breast until the ends overlap and then place the chicken into a greased baking dish.
Bake for 20 minutes or until the chicken is fully opaque and reaches at least 165°F (75°C).
For the chipotle sauce, add the tomato sauce, chipotle peppers, tomato paste, lime juice, and the remaining spice mixture to a blender and puree until smooth.
Pour the sauce over the cooked chicken roll ups and sprinkle with more cotija cheese.
Broil for 5 minutes or until the sauce bubbles and the cheese melts and browns slightly.
Serve with cooked rice, avocado, sour cream, and/or pico de gallo.