
Heat the oil in a large pan to medium heat and add the onions and jalapeno peppers. Cook them down about 5 minutes.
Add the garlic and stir. Cook for 1 minute.
Season the chicken breast (or thighs) with salt and pepper, then add them to the pan. Give them a nice sear on each side, a couple minute each.
Process the tomato sauce and chipotles in adobo sauce in a food processor, then pour the mixture into the pan, covering the chicken.
Stir in the seasonings.
Bring to a quick boil, then reduce the heat and simmer for 30 minutes, or until the chicken is cooked through and easily pulls apart.
Remove the chicken and shred it with a couple of forks.
Return the chicken to the pan and simmer in the sauce another 5 minutes.
Heat oven to 350 degrees F.
Spread the tortilla chips over a large baking sheet, baking dish or pan, or large oven safe bowl.
Top the tortillas with shredded chipotle chicken, then top with shredded cheeses.
Bake for 10 minutes, or until the cheeses are nicely melted.
Garnish with your favorite toppings and serve!