Melt the butter and add the onions, sugar, and 1 teaspoon salt, then simmer in a hot pan just to sear them and get color on the outside (this gives it great flavor). Turn the heat down to low-medium-ish heat, cover and cook 'til onions are translucent, about 15 minutes, then uncovered for another 15 minutes. Stir occasionally and scrape the goodies off the bottom. Turn the heat down as needed (don't let them burn obviously) and cook longer if they're not a deep brown and caramellized yet.
Now add the wine and cook 1-2 minutes. Add broth, bay leaves, thyme, the other 3/4 teaspoon salt and pepper, and simmer for 30 minutes to allow all the flavors to come together nicely. Discard any bay leaves or thyme sprigs. Taste test to see if it needs more salt and pepper. Using a largle ladle or glass measuring cup, divide soup evenly between 6 oven-safe bowls. Sprinkle parmesan on the soup, place croutons or toasted bread on the parmesan, then add the provolone, gruyere or whatever cheese you're using for the top.
Place a cookie sheet on your oven rack and then set the bowls on and bake about 10 minutes at 450* 'til cheese is melted and everything is bubbly. You might want to turn on your oven's broiler to get the cheese a bit golden on top. Let cool a few minutes before serving.