Place the sausages in a big pan and drizzle with 1 tablespoon olive oil. Raise the heat to medium and cook, stirring occasionally, for 5 to 7 minutes, or until each side is gently browned. While you cook the peppers and onions, remove from the heat, cover, and let it rest.
Heat two tablespoons of olive oil in the same skillet over medium heat. Add the onion and a teaspoon of salt for seasoning. For ten minutes, sauté the onion. Turn the heat down to medium-low if the onions begin to brown too quickly.
Stir in the pepper flakes, garlic, bell peppers, and the remaining ½ teaspoon of salt. Simmer the peppers for ten to fifteen minutes, or until they are tender but still somewhat crunchy. To scrape off any cooked pieces from the bottom of the skillet, add the balsamic vinegar and stir. Before serving, return the sausages to the pan, lower the heat to low, and cover the pan with a lid to allow the sausages to reheat for a few minutes.
Use a low broiler or a toaster oven to gently cook the hoagie buns. Cover with coarse mustard, mayonnaise, or pesto mayonnaise, as preferred, then stuff with sausage, bell peppers, and onions. To melt the cheese, add it on top and put it back in the toaster oven or under the broiler.