Combine ingredients for Fajita marinade in a large mixing bowl and whisk well. Add chicken to the marinade and let it marinade for about 15 minutes.
Preheat an oven-safe skillet on stovetop, medium heat.
Add chicken and the marinade to the skillet and cook until chicken is fully done, flipping it half way through.
While the chicken is cooking, prepare Spanish rice according to the package and set aside.
Take chicken breasts out and lay them on a cutting board. Dice the chicken once it is cooled enough to handle.
Saute chopped onions and tomato in the same skillet.
In a large, clean, mixing bowl, combine Spanish rice, diced chicken, sauteed onions and tomato (including the marinade that was leftover in the skillet) and cilantro. Mix well and taste to see if you need to add a little more salt.
Preheat the oven to 375.
Cut the bell peppers in half, lengthwise, and clean them out, taking out all the seeds and membrane.
Lay the bell pepper halves in the skillet, like little cups, and fill them with the rice/chicken mixture.
Sprinkle about 1-2 tablespoons of cheese on top. Place the skillet in the oven for 15-20 minutes, until the peppers are cooked.