If baking right away, heat oven to 375 degrees. If freezing, prepare an aluminum or foil lined pan.
Heat oil in a saute pan over medium heat.
Saute the diced onion and garlic until translucent and browned, about 5-7 minutes. Set aside.
Meanwhile, pulse enchilada sauce and 1-3 chipotles in a food processor until pureed.
Pour a small amount of sauce in the baking dish so the enchiladas don't stick.
In a medium bowl, put in shredded chicken, taco seasoning, and 1 cup cheese.
Mix well and add 3/4 cup of enchilada sauce.
Place a little less than 1/2 cup of the chicken mixture onto each flour tortilla.
Roll the tortilla up and place seam side down in the baking dish. Repeat for all tortillas.
Pour the remaining enchilada sauce on top, pushing down in between the tortillas.
Sprinkle the remaining 1 cup of cheese on top.
Bake at 375 for 25-30 minutes or until bubbly.
If freezing, cover with foil.
Reheat covered at 375 degrees for 45 minutes, then uncover and heat another 15 minutes.
Spicy chicken enchiladas should be warmed through and bubbling.
Serve with cilantro, sour cream, guacamole, and salsa.