Wipe roast dry with a paper towel and sprinkle with 2 teaspoons of the salt, pepper and flour, shaking off excess flour.
In a large nonstick pan, heat the extra light olive oil over high heat for 2 to 3 minutes, until very hot. Add beef roast and brown well on all sides. Transfer meat to a baking dish and set aside.
In a large stockpot, heat the extra virgin olive oil over medium heat, for about 2 minutes. Add onions, bay leaves, red pepper flakes, dried thyme, chopped parsley, chopped basil, chopped rosemary and remaining salt. Cook, stirring well, for about 8 to 10 minutes until the onions are soft.
Increase heat to high, add the Marsala wine and bring to a boil, stirring well, and cook for 5-8 minutes until liquid has reduced by half. Add browned roast, the accumulated juices and beef broth. Bring to a boil. Then simmer for 1 hour and 35 minutes, turning the meat every 15 minutes and stirring the contents to prevent sticking.
Remove meat and cover with foil. Remove bay leaves from sauce. Bring sauce to a boil, and then lower heat to medium-high and cook, stirring well, for 30 minutes, or longer if you prefer a thicker sauce.
Slice the roast and gently reheat slices in sauce over medium-low heat. Serve, topped with some of the sauce, on a large platter. Serve the extra sauce on the side.
Optional
To complete the sauce, add the cheese, stirring well until it has completely melted into the sauce.