In a large saucepan, sauté onions with butter on medium-high heat until well browned, about 50 minutes (or longer) stirring occasionally. Add sugar about 10 minutes into the process to help with the caramelization.

When onions are caramelized, add garlic and sauté for 1 minute; add flour and stir for one minute. Stir in wine, scrapping up any browed bits, cook for 2 minutes. Add stock and thyme. Reduce heat, cover partially and simmer until the flavors are well blended, about 30 minutes. Season to taste with salt and pepper. Remove thyme and discard.

Ladle soup into individual, oven-proof bowls. Cover with toast and top toast with cheeses. Broil for 2 to 3 minutes, or until the cheese bubbles and is slightly browned. Serve immediately.