To a blender, add the entire can of chipotle peppers and adobo sauce, garlic cloves, chili powder, cumin, salt, dried oregano, smoked paprika, black pepper, and water. Blend until smooth, about 1 minute.
Place the chicken in a small dish and completely cover it with the sauce. Cover the dish and marinade the chicken in the fridge for 30 minutes or up to 1 day in advance.
Preheat the oven to 400 degrees F. Heat the oil in a skillet that has a lid over medium heat. Set aside a 9x13-inch baking dish.
Sauté the onion until lightly browned and softened, about 5 minutes.
Add the chicken to the skillet, reserving the marinade. Cover and cook for 8 minutes. Flip and cook, uncovered, for another 6 to 8 minutes until the chicken has reached an internal temp of 165 degrees F. Remove the chicken to a cutting board and chop it into bite-sized pieces.
Add 1/4 cup of the marinade and 1/4 of water to the skillet and simmer the sauce for at least 5 minutes or until the sauce thickens. Turn off the heat.Note: It is important that you simmer for at least 5 minutes to ensure you've killed any bacteria from the chicken.
Add the chopped chicken and cilantro to the skillet. Toss to coat in the sauce.
To assemble the tacos, place the taco shells in the 9x13 baking dish. Add about a tablespoon of refried beans to the bottom of each taco shell. Evenly distribute the chicken between the shells. Finally, cover each taco with shredded cheese.
Bake the tacos for 5 minutes. Add whatever toppings you like (ideas in the notes) and enjoy!