Did you use crocks or just regular bowls, or what? Did you use the "Best" or "Quicker" recipe?
Here's the adapted recipe (reworded to avoid copyright issues):
Soup
3 tablespoons unsalted butter , cut into 3 pieces
6 large yellow onions (about 4 pounds), halved and cut pole to pole into 1/4-inch-thick slices
Table salt
2 cups water , plus extra for deglazing
1/2 cup dry sherry
4 cups low-sodium chicken broth (see note)
2 cups beef broth (see note)
6 sprigs fresh thyme, tied with kitchen twine
1 bay leaf
Ground black pepper
Cheese Croutons
1 small baguette , cut into 1/2-inch slices
8 ounces shredded Gruyère cheese (about 2 1/2 cups)
Instructions:
Preheat oven to 400, with rack in lower-middle position. Spray the inside of a dutch oven with nonstick spray, and add butter, onions and 1tsp salt. Cook for an hour, covered, and then remove and stir, scraping the pot. Put it back in the oven with the lid off just a bit and cook for another 90-105 minutes, scraping at the hour mark, until the onions are brown and very soft.
Remove the pot, put it over medium-high heat, and keep cooking for about 15-20 minutes, or until all the onions brown and the liquid evaporates. Keep cooking for another 6-8 minutes until you have a dark crust on the bottom, and then add 1/4 cup water and deglaze. Repeat this deglazing/evaporating process two or three times, and then stir in the sherry and let it cook until it evaporates again.
Add the broth, two cups of water, thyme, bay leaf, and 1/2 tsp salt and deglaze again. Bring to a simmer over high heat, and then reduce the heat back down and let it simmer, covered, for 30 minutes. Toss the herbs and season with s+p.
To make the croutons, bake the baguette slices on a cookie sheet in a 400 degree oven for about 10 minutes, until dry and golden.
Service: Fill broiler-safe crocks with soup, top with baguette slices, sprinkle with gruyere, and broil (6" or so from the element) for about 3-5 minutes until the cheese is melted bubbly, and then let it cool for another 5.