In a large stock pot over medium-high heat add chopped onions and butter. Add 1 teaspoon of salt to the onions. Saute the onions for about 20 minutes, or until they have become golden brown. Add 1 tablespoon of flour, and stir to coat the onions with flour. Cook for the flour for another minute or until it becomes fragrant like pie crust.
Add in the beef stock, chicken stock, beef base, and thyme. Reduce heat to a low temperature. Cook the soup for another 15 to 20 minutes.
Before serving top with croutons and shredded cheeses.