Heat the olive oil in a large, deep pan.
Cut your guanciale or bacon into 1/2" cubes and then once the oil is hot, add it to the pan on low heat. Stir occasionally. Cook until it is golden brown, but not super crispy. Using a slotted spoon, remove the guanciale or bacon from the pan and add it to a bowl to use later. Leave the fat in the pan.
Add your sliced onion to the pan and cook on medium low heat until the onions are starting to get golden brown. This should take about ten minutes. While this is cooking, start boiling your water. Once the onions are starting to get golden brown, add in your wine and continue to cook for 3 minutes. Then add in your crushed tomatoes, red pepper flakes, guanciale (or bacon), 1/4 teaspoon of black pepper and 1/2 teaspoon of salt. Cook for about 10 minutes, until the sauce is getting thick. You will be adding some pasta water to it later on
Once the water is boiling, add your penne, half of your pecorino cheese, plus 1 tsp of salt. Stir, and cook until al dente (about 8-9 minutes)
Add your cooked pasta to the sauce with 1/2 cup of pasta water. Cook for 2 minutes and taste. Add additional salt or pepper if needed. When you are serving the pasta, add a little bit more pecorino to each bowl.