Place the rinsed tomatoes and tomatillos in a medium saucepan and cover them with water. Set the saucepan over medium heat. Once it comes to a simmer, cook for 8 to 10 minutes, or until the tomatoes and tomatillos are soft, thoroughly cooked, and smooshy but not coming apart. Remove them with a slotted spoon. Place in the jar of a blender or food processor and blend until smooth.
Heat the oil in a large and deep pan over medium heat. Once it is hot but not smoking, stir in the onion and cook until soft and translucent, for about 5 to 6 minutes. Stir in the garlic and cook until it becomes fragrant and lightly browned, about 1 minute.
Pour the tomato/tomatillo sauce on top and sprinkle the oregano, marjoram, thyme, salt and black pepper. Spoon in the chipotle Chiles in Adobo sauce. If you want it spicy, you may drop a whole Chipotle Chile in Adobo in there as well. Let the sauce simmer, stirring now and then until it seasons and deepens its red color, about 10 to 12 minutes. You may want to partially cover the pan as the sauce may want to jump out over your burners.
Toss in the chicken and combine with the sauce. Let it cook, stirring casually, until the chicken has absorbed almost all of the juices and the mix is moist but not juicy.