Place onion, garlic, tomatillos, green bell pepper, cumin seeds, oil, ½ tsp salt, and ¼ tsp in a slow cooker. Toss together. Pour in broth or water. Place chicken thighs on top, skin side up. Cover and cook on low for 6-8 hours until bubbling and chicken is easily shreddable.
Remove chicken thighs to a cutting board and set aside to cool.
Place contents of the slow cooker into a blender. Add cilantro and jalapeño. Blend until smooth.
Remove skin and bones from chicken thighs. Shred chicken meat with two forks.
Preheat oven to 350°. Butter a large casserole dish or 9x13-inch pan. Spread about ¼ cup of salsa verde in the bottom of the pan. Pour the rest into a shallow bowl.
Heat a cast-iron skillet over medium heat. When skillet begins to lightly smoke, heat tortillas one at a time for 10-15 seconds per side then wrap in a towel to keep warm.
Working one at a time, dip tortillas in salsa verde, place on a plate, and fill with chicken, pinto beans, and Monterey or cheddar cheese. Roll into tight cylinders and place in the prepared pan side-by-side.
Top enchiladas with remaining salsa verde. Sprinkle with quest fresco. Cover with foil and bake for 15 minutes. Remove foil and bake for an additional 10-15 minutes, until cheese is melty.
Allow to cool for 5-10 minutes before serving. Garnish with pepitas, salsa roja or hot sauce, and cilantro, as desired.