Pre-heat the oven to 350. Lightly mist a 9x13 baking dish with cooking spray and set aside.
In a medium bowl, mix together the tomato sauce, vinegar, garlic, chili powder, cumin, oregano, sugar, salt and pepper until thoroughly combined.
In a large skillet or sauté pan, bring the oil to medium-high heat. Add the chopped onions and cook for a couple minutes until they start to soften and become fragrant. Add the chicken breasts in a single layer and cook for 3 minutes on one side, flip them over, and then continue to cook for 3 minutes on the other side. Add the tomato sauce mixture to the pan and bring it to a boil. Lower the heat to medium-low and cover the pan. Simmer for about 20 minutes until the chicken is fully cooked through.
While the chicken is cooking, boil water and cook the pasta shells according to package directions. Drain and set aside to cool.
Remove the lid from the pan and transfer the chicken breasts to a cutting board, leaving the sauce. Add the can of enchilada sauce to the sauce in the pan and stir to combine. Reduce heat to low and recover until needed.
Shred the chicken using two forks and transfer it to a large bowl. Add ½ cup (2 ounces) of the shredded cheddar, the black beans and ½ cup of the sauce from the pan. Stir until well combined.
Spread ½ cup of the sauce from the pan across the bottom of the prepared baking dish from step one. Using the chicken filling from step 5, stuff the cooled pasta shells evenly with filling and place them on top of the sauce in the prepared baking dish. Once the shells are in place, pour the remainder of the sauce from the pan over the tops of the stuffed shells and follow with the remaining shredded cheddar cheese. Place in the oven and bake for 30 minutes until the dish is heated through and the cheese is melted.