Set a perforated baking sheet or a fine-mesh rack over a rimmed baking sheet. Place tomatoes on perforated baking sheet; sprinkle with sugar and salt. Cover and transfer to refrigerator; let stand overnight to drain.
Transfer tomatoes to a large bowl; set aside. Discard liquid. Place garlic, lemon peel, orange peel, thyme, oregano, and olive oil in a large saucepan over medium-high heat. Cook until heated through. Pour garlic mixture over tomatoes. Cover and transfer to refrigerator; let marinate overnight. At this point, tomatoes and marinade may be stored, covered and refrigerated, until ready to use, up to 2 weeks.
To use tomatoes, remove from marinade and finely chop; reserve marinade for another use.