1. In a large skillet, heat 1 tablespoon oil over medium-high heat. Add 1 bag of onions, the bay leaf and 1 thyme sprig. Cook, stirring occasionally, until onions begin to turn deep golden brown in spots, 6 to 8 minutes. Transfer to a bowl with a slotted spoon. Repeat with remaining 1 tablespoon oil, onions and thyme sprig. Return first batch to skillet.
2. In a small bowl, stir together vinegar, wine, sugar and salt. Add to onions and bring to a boil. Reduce heat to medium-low and simmer, stirring occasionally, until liquid is the consistency of a syrup and onions are glazed, 20 to 25 minutes. Discard bay leaf and stir in pepper. Garnish with thyme.