Place chicken thighs in a bowl and season with salt and pepper. Next, dust chicken with flour. Heat the stove to high. Add 1 tbsp of oil to a large skillet and brown chicken on all sides in oil, about 4-5 minutes per side. Remove chicken to platter.
Add the remaining tablespoon of oil to the same skillet and cook and stir the onion, pepper and mushrooms for 5 minutes, or until softened and fragrant. *You can also do these steps in your slow cooker if it has a saute function.
Add tomatoes, marinara sauce, tomato paste, herbs, and garlic to the slow cooker. Stir to combine.
Next, add the chicken and vegetables to the slow cooker and toss gently to coat in sauce. Cook for 6-8 hours on low or 3-4 hours on high. Season with salt and pepper to taste.
Serve over pasta, zucchini noodles, spaghetti squash or rice and garnish with Parmesan cheese, if desired.