In a heavy soup pot, melt the butter. Add the onions and shallots. Cook over low heat, stirring occasionally, for 1 hour or until the onions are caramelized.
Sprinkle the onion mixture with the flour. Cook, stirring, for 2 minutes or until the flour is absorbed.
Add the wine, stirring constantly, then the stock and water. When the mixture comes to a boil add the bay leaves, salt, pepper, and Kitchen Bouquet.
Turn down the heat, cover the pot, and let the soup simmer for 1 more hour. Taste for seasoning and add more salt and pepper, if you like.
Set the oven at 400. Ladle the soup into the Onion Soup Bowls. Arrange 2 slices of baguette on top of each, and sprinkle with cheese.
Set the bowls on a rimmed baking sheet. Cook the cheese until the top forms a golden crust.
