In a large skillet, cook ground beef, stirring to crumble. Drain and set aside.
Sauté jalapeno pepper and 1/2 cup on onion in hot oil until tender. Add tomato sauce, both cans of tomatoes, sugar, salt, and pepper; stir well. Bring mixture to a boil, then reduce heat and simmer for 15 minutes, stirring occasionally.
Combine flour with the 1 tablespoon water; stir until smooth. Stir into tomato mixture and cook, stirring, for 1 minute. Combine 1 1/2 cups Cheddar cheese and 1 1/2 cups Monterey Jack cheese and remaining 1 cup onion; set aside remaining (1 cup total) of cheese for topping casserole.
Using tongs, dip a tortilla into hot tomato mixture. Sprinkle about 2 tablespoons of ground beef and 1/4 cup of the cheese and onion mixture down the center of each tortilla. Roll up jellyroll fashion then place, seam side down, in a lightly greased 13x9x2-inch baking dish. Repeat with remaining tortillas. Spoon remaining sauce over tortillas. Cover dish with foil and bake at 350° for 25 minutes. Uncover, sprinkle with remaining cheese, then bake 5 minutes longer, or until cheese melts.
Calories per serving: 606