1. Preheat oven to 350 degrees F. Place black beans, chipotle peppers, onion, pepper, and water in a large skillet. Heat over medium low heat, mashing beans and chipotle peppers to break them up, for about 15 minutes. Add a bit more water if you need to, it should have the constancy of refried beans more chunky.
2. Heat enchilada sauce, and pour about 1/2 in the bottom of a 9x13"pan, to cover the bottom. To prepare tortillas, place on a plate and cover with a damp towel. Microwave for 1-2 minutes, until they are hot and very flexible.
3. Place about 1/4-1/2 cup filling along the middle of the tortilla and roll it over to make a filled tube. Place into the pan. Repeat with the rest of the tortillas.
4. After filling all the tortillas and placing them in the pan, cover with remaining enchilada sauce. Use a spoon to make sure everything is covered and wet. Put cheese sauce on top. Place in oven for about 1/2 hour, or until the top is browned.