Preheat oven to 350 degrees. Spray 9X13 pan with cooking spray; set aside.
Lay out tortilla with widest part facing you. Spread a thin layer of refried beans across bottom 3/4ths of tortilla; layer black beans on top of refried beans; next sprinkle with green onions. Top with mounds of pepper jack cheese. Fold side of tortilla inward; fold bottom around sides and mixture and continue to roll making sure side of tortilla are kept folded inward.
Lay tortilla seam side down in baking pan. Continue with other tortillas until pan is completed. Sprinkle with green onions. Cover with enchilada sauce. Cover top completely with cheddar cheese. Cover with aluminum fold that has been sprayed on the inside with cooking spray (so cheese will not stick) and bake approximately 20 minutes.