In a medium size saucepan, melt butter over medium heat. Add onion; cook 3-5 minutes, stirring frequently, until tender. Reserve 1/4 cup enchilada sauce; add remaining sauce to the onion. Stir in cumin and chicken. Reduce heat to medium-low; simmer uncovered for 5 minutes.
Lightly grease 10 inch skillet with butter or cooking spray; heat over low heat. Place 1 tortilla in skillet; top evenly with pepper jack cheese and second tortilla. Spread chicken mixture over second tortilla; top with third tortilla. Sprinkle evenly with cheddar cheese, top with jalapeno and green chilies. Place fourth tortilla over chilies; spread reserved 1/4 cup enchilada sauce over top.
Cover skillet; cook over low heat for 18-20 minutes or until thoroughly heated. Remove from heat; let stand for 10 minutes before serving. Cut into 4 wedges; serve topped with sour cream if desired.