Preheat oven to 350 degrees. Grease 6-2 ½ cup oven proof containers or a large casserole dish (to hold 12 cups).
Roasting the Chile Peppers: Place the chile peppers on a baking sheet underneath the broiler. Checking often, allow to blacken on each side. Remove from oven and place either in a plastic zipper bag OR in a heatproof bowl and cover with plastic wrap. Place in the refrigerator for 15 minutes. After 15 minutes, remove from container or bag and remove the blackened skin by rubbing or pulling it off leaving only the soft flesh of the pepper. Remove top with stem, slice vertically and scrape out the seeds with a dinner knife (non sharp). Chop and set aside. Wash hands thoroughly after handling the chilies and if choosing hotter varieties consider wearing protective vinyl or latex gloves.
Boil water and prepare pasta to package instructions.
While pasta is cooking, melt 1 ½ teaspoons butter in a medium skillet over medium to medium-high heat. Add onions and sauté until they are translucent; about 5 minutes. Set aside.
In a medium saucepan over medium heat melt the 3 tablespoons butter. Whisk in the flour, as well as salt and pepper. When it is well combined, slowly pour in the milk whisking the whole time to avoid burning the mixture. Continue to whisk until the mixture begins to thicken noticeably (5-10 minutes).
Add the cheese (both types) to the flour/milk mixture and stir constantly until cheese has melted.
When pasta is cooked, rinse, drain well and return to the cooking pot. Pour in the cheese sauce, cooked onions, roasted chilies and chopped chicken; stir well to fully combine. Add more salt and pepper to taste if needed. Spoon into cooking container(s). If cooking in personal size containers cook 30 minutes and 40 minutes if in a casserole dish or until the macaroni develops a nice, brown crust on the top.
Remove from oven to cool slightly and serve.