Place large, nonstick pan over medium heat heat. Add 1 tablespoon butter to the pan. Sprinkle salt and pepper over both sides of the chicken. Add to the preheated pan and brown on both sides and thoroughly cooked to 165 degrees F. Transfer browned chicken to a plate and cover with foil.
To the hot pan, add other tablespoon butter and 1 tablespoon olive oil. Add onions, thyme, bay leaves, salt and pepper to the pan and stir to coat in spices, butter and oil. Cook slowly, stirring occasionally for 20-30 minutes or until completely soft and tender. If your onions are coloring before they are tenderizing, your heat may be too high. Reduce heat and continue cooking.
Once onions are completely tender and browned all the way though, deglaze pan with marsala wine and cook down by half (this shouldn't take too long.) Add in the beef broth. In a small bowl, stir butter and flour together to create a paste. Add to pan to thicken the gravy. Stir and cook 1 minute. Reduce heat to low.
Add in chicken and cover to warm through, about 3 minutes. Add shredded gruyere cheese to chicken and cover to melt completely, another minute or two.
Top chicken with dried parsley and cracked black pepper, if desired and serve hot.