Preheat oven to 450 degrees.
In a large bowl, combine the onion, garlic, tomatoes, olive oil, pepper flakes, 2 Tablespoons of herbs and 1 teaspoon salt; toss until everything's nicely mixed. Season the chicken thighs on both sides with salt (and pepper if you'd like) to taste.
Arrange the chicken thighs on two heavy rimmed baking sheets, with space between the chicken pieces. Distribute the tomato mixture and any juices around the chicken so it's in an even layer but not covering the chicken.
Roast until the chicken is totally tender when pierced with a knife (or reaches 170 degrees on an instant-read thermometer), 35 to 45 minutes. During roasting, check that the tomato mixture isn't burning. You want the vegetables to release juices, collapse and brown slightly but not to burn onto the pan. If they're getting too dark, pour in a few spoonfuls of water or chicken broth.
When the chicken is done, transfer to serving platter. Put a large sieve/colander/strainer over a bowl and very carefully scrape the tomato mixture into the sieve. Make sure you catch all of the juices, which are delicious. If there are browned juices on the baking sheets, deglaze them by pouring a bit of water or chicken broth or reserved juices, and scraping to dissolve. Add this liquid to the vegetable juices in the bowl.
After the vegetables drain for a few minutes, arrange on the chicken platter as an accompaniment. Sprinkle everything with the remaining 1 tablespoon herbs and serve. pass a bowl of the juices at the table to drizzle over the chicken and vegetables. Or refrigerate them for use in another recipe if you'd like, such as soup.
To reserve leftovers: Pour the vegetable juices into a measuring cup, cover and refrigerate (the fat will solidify on the top for easy removal the next day) Depending on appetites, you should have a bout 4 thighs left over, wrap and refrigerate , along with the reserved tomato mixture.