Heat oil in large pan on medium low heat. Add onions and cook uncovered 5 minutes. You want the onions to soften and not brown too quickly. Add peppers, garlic, salt, pepper and red pepper flakes. Cook about 10 minutes.
Remove onion/pepper mixture from pan and keep warm. To same pan add sausages and raise heat to medium. Cook sausages on all sides until brown. Add water and marinara sauce and cover pan. Bring to a simmer, lower heat and cook for 10 minutes. Uncover the pan, cook a few minutes more to let most of the liquid evaporate.
Remove sausages from pan and either leave whole or slice. I like to slice mine into 1/4 inch pieces. Mix sausages with pepper and onion mixture and serve on toasted Italian bread or sub rolls. I love mine topped with mustard.