Coat a large saucepan with olive oil. Add the guanciale and saute over low heat. Cook until it is brown and crispy and has rendered a lot of fat. Remove and reserve 1/3 of the guanciale for garnish. Bring the pan to a medium heat and add the onions and crushed red pepper. Season generously with salt, to taste. Cook the onions until they are translucent, starting to turn golden and are very aromatic. Add the tomatoes and bring to a boil, then reduce the heat and simmer the sauce for about 1 hour, tasting periodically. Adjust the salt, as needed.
Bring a large pot of well salted water to a boil over high heat. Add the pasta and cook for 1 minute less than the instructions on the package. Remove 3 or 4 ladlefuls of the sauce from the pot to a bowl, as an insurance policy. You can always add it back in but it's harder to take out once the pasta is in the pan. You're looking for the perfect ratio between pasta and sauce. Drain the pasta from the water and add to the pot of sauce. Stir to coat with the sauce. This is how you always finish pasta; you cook it in the sauce to perform the marriage of the pasta and the sauce. Add more sauce, if necessary. Add in the cheese and drizzle with olive oil to really bring the marriage together. Toss to coat and serve in shallow bowls garnished with cheese and the reserved guanciale. Sprinkle with chives to finish, if using.