Preheat oven to 325 degrees F.
Add the onions to a large bowl, cover with hot water and allow to sit for about 5 minutes. This is to help make peeling the onions much easier. Strain onions and peel.
In a small bowl, whisk together the 1/4 cup oil, vinegar, honey, thyme, salt and pepper until combined. Put the onions in a large bowl, pour the dressing over them and toss well to coat.
In a large saute pan over medium-high heat, add about 2 tablespoons olive oil and heat. Once hot, add the onions. Next place the saute pan into the preheated oven and roast for 18 to 20 minutes until the onions are soft and slightly caramelized.