Rinse the beans in a colander or strainer under cold running water. Pick out any stones or bad beans. Put the beans in a medium-size saucepan and cover with water plus two inches. Soak over night.
Drain the beans very well by tilting the pan to its side with the cover ajar. Pour in just enough water to barely cover the beans, and add two onions, two cloves of garlic, oregano, cumin, bay leaves, salt and pepper. Cover the pan, bring to a boil, then reduce the heat to a simmer. Cook the beans until they are tender, about one hour, stirring occasionally. (Note: The point is to have the beans absorb most of the liquid by the time they are done. so that they have a thick sauce-like consistency. If they aren't done and more water is needed, add just a little and check the beans again when most of it is absorbed. The beans should still retain their shape when they are done.) Discard the bay leaves.
Mash about one-quarter of the beans against the sides of the pot and stir to blend them. Set aside to cool.
To make the sauce: In a large skillet heat olive oil. Add the remaining onions and garlic and cook over medium heat for ten minutes, or until tender and limp, stirring often. Add the tomatoes with their juice, tomato paste, water, chilies, and jalapeño pepper, and stir to blend. Cook for five minutes, or until the sauce has thickened. (May be prepared to this point up to twenty-four hours in advance. Cover and chill the sauce and beans separately.)
To assemble the enchiladas: Spoon a little of the sauce into the bottom of a large baking dish or two medium-size dishes. Place a tortilla on your work surface and spoon about two tablespoons of the bean mixture down the center. (It's good to dived the filling beforehand.) Cut a slice of the into tow or three pieces and place on top of beans. Roll the tortilla and place it seam side down in the baking dish. Repeat with the remaining tortillas.
Spread the sauce evenly over the enchiladas. Top each enchilada lengthwise with some of the shredded cheese. This helps identify the enchiladas when you are dishing them out. Bake in a 350º oven for twenty to twenty-five minutes, or until hot and bubbly.