Combine the onion, jalapeno and oil in a large saucepan over medium heat.
Cook, stirring often, until the onions and peppers have softened, 8-10 minutes.
Stir in the garlic, chili powder, cumin and sugar, and cook just until fragrant, less than 30 seconds.
Mix in the tomato sauce, water, and chopped tomato.
Bring the sauce to a simmer, lower the heat and cook until slightly thickened, about 5 minutes.
Nestle the chicken into the sauce. Reduce the heat to low, cover and cook until the chicken is completely cooked through (160? F on an instant-read thermometer), about 12-20 minutes.
Transfer the chicken to a plate and set aside to cool.
Strain the sauce through a large mesh strainer into a medium bowl, pressing down on the onions and tomatoes to extract as much liquid as possible.
Transfer the reserved solids to a large bowl and set aside.
Season the sauce with additional salt and pepper to taste.
Shred the chicken into bite size pieces and add to the bowl with the onion mixture.
Add in ¼ cup of the enchilada sauce, ½ cup of each of the shredded cheeses, and the cilantro.
Stir to combine.
Preheat the oven to 425 F.
Oil a 9 x 13 baking dish with cooking spray.
Stack the tortillas on a plate, cover with plastic wrap, and microwave for 40-60 seconds, until warm and pliable.
Spoon 1/3 cup of the chicken mixture evenly down the center of a tortilla. Roll up the tortilla around the filling tightly, and place in the prepared baking dish, seam-side down.
Repeat with the remaining filling and tortillas.
Lightly spray the tops of the enchiladas with cooking spray. Place in the oven, uncovered, for 7 minutes or until the tortillas start to brown slightly
Reduce the oven temperature to 400 F. Remove the enchiladas from the oven and pour the sauce oven the top.
Sprinkle with the remaining shredded cheese.
Cover the dish with foil and bake for 20 minutes.
Remove the foil and bake for 5 more minutes, until the cheese is browned.
Remove from the oven and let stand 10 minutes before serving.