Saut onions, garlic, with seasonings: Once you've started to heat the water, start working on the sauce. Heat olive oil in a very large skillet on medium heat. Add the chopped onion, oregano and red pepper flakes. Cook for 5 minutes, stirring occasionally, until the onions are softened. Add the garlic, thyme, season with salt and pepper. Cook for an additional minute, until the garlic is fragrant. Remove from heat and set aside.