In a large Dutch oven, combine the onions, oil, salt and sugar.
Cook over medium-high heat, stirring very often for 30 minutes.
As the onions begin to stick to the pan and create fond or browned bits, deglaze the pan with a couple tablespoons of water. You may add as much as 1 cup over the full cooking time.
Add the garlic and continue cooking, stirring often, for an additional 15 minutes until deep amber.
Deglaze the pan with the marsala and cook until fully absorbed.
Add the thyme and beef stock and bring to a gentle simmer.
Meanwhile, preheat the oven to 400 degrees.
Lay the baguette medallions on a sheet pan and drizzle with some oil.
Bake until very crispy, for about 10 minutes.
Turn on the broiler.
Divide the soup into 4 large ramekins or soup crocks.
Place a few pieces of toasted baguette over the soup and top with 2 slices of the cheese.
Broil until the cheese begins to caramelize and blister, for a minute or two.