In a small pot, melt the butter over medium-low heat. Once the butter is melted, slowly mix in the flour until you have a thick consistency. Set aside and keep warm until ready to use. This is the roux.
In a 3-gallon stock pot, melt 4 tablespoons of butter. Once the butter is melted, add the garlic, celery, and onions along with the bay leaves, salt, and white pepper. Cook the mixture until it is lightly browned, stirring it occasionally. Add the clam juice, stir, and let it cook until it is moderately warm. Then add the potatoes and bring the chowder to a boil, stirring it occasionally. Once the soup is boiling add the chopped clams, bacon, cream, and thyme. Stir the soup and let it cook until hot, do not bring it to a boil. Remove the soup from the heat and slowly stir in the roux until the desired consistency is reached.