Fill a large pot with water and add salt. You’ll be bringing it to a boil to cook the pasta when the sauce is almost done.
In a 12-inch skillet or a Dutch oven, heat the olive oil to medium to medium-high heat (every stove is different). Add the thinly sliced shallots (or whatever onion you are using). Begin to stir and season with some salt. Add the sugar. Keep stirring (don’t leave the pan!) and after the first 5-7 minutes, add a bit of water to deglaze.
Continue cooking and stirring, adding water every few minutes or so (you know when the shallots dry up again. This helps to prevent burned shallots).
Once they are a nice and golden brown (could take between 15-30 minutes), stir in garlic (if you’re using). Add the balsamic vinegar and coconut aminos. If needed, add a bit more water to deglaze and keep stirring until the garlic is soft and a nice golden color).
Add in the anchovies and red pepper flakes (if you’re making this spicy). Stir the anchovies into the shallots. They will dissolve pretty quickly and combine with the shallots.
Add the tomato paste and stir constantly, cooking the paste until it changes from bright red to a deeper and darker or until the paste has caramelized and become darker, 2-3 minutes. If you’re adding sauce, this is when you add about 1 cup of tomato sauce (I liked adding the sauce as I feel it makes it smoother. But you could do without sauce and just add the reserved pasta water). Taste the sauce and add a little more salt (if needed)and some freshly ground pepper. At this point, the sauce is almost ready, so it’s time to cook the pasta.
Bring the large pot to a boil and add your pasta. Cook according to the pasta directions, but you are making the pasta al dente (I usually cook it a little less than al dente because I am combining the pasta with the sauce in a hot pan and it will continue cooking a little more).
When pasta is ready, drain (reserve about 1 cup pasta water). Add the pasta to the skillet with the sauce and use tongs or a spoon to combine the pasta in the sauce. If you added some tomato sauce to the shallot mixture the sauce should be a nice texture, and you may need only about 1/4-1/2 cup pasta water.
If you didn’t add tomato sauce, add some of the reserved pasta water (you’ll probably use a whole cup) and stir together with the pan on the heat (be sure not to keep it too long on the heat as you don't want the pasta to overcook and get mushy). Check the seasoning and add more salt, if needed, and freshly ground pepper.
The stove should be on a medium-high heat and this shouldn’t be for more than 2 minutes (that’s why I like to undercook it before al dente readiness).
Add the pasta to a serving bowl or platter. Drizzle on some really good extra-virgin olive oil.
Serve the pasta and sprinkle on some chopped Italian parsley and red pepper flakes (if you’re using). Enjoy!