Melt 4 tablespoons butter in a large pot over medium-high heat. Add onions and season with 1 teaspoon salt, 1/2 teaspoon black pepper, bay leaves and thyme. Cook until softened, the liquid has evaporated and the onions have browned, about 45 minutes to an hour. Add the wine and cook until it has fully absorbed. Stir in the stock and add 1 cup of water. Bring to a simmer and then cook until slightly reduced, about 30 minutes. Season with the remaining 1/2 teaspoon salt and 1/4 teaspoon black pepper. Lower heat and keep warm.

In the meantime, set a medium saucepan over moderate heat with 2 tablespoons butter. Once melted, whisk in the flour and cook 30 seconds. Slowly whisk in the milk and cook until thickened. Season with salt, pepper, mustard and cayenne. Remove from heat and stir in 1 cup gruyere and cheddar cheese until melted; add prepared macaroni noodles, stir to combine.

Divide the soup between six oven-safe ramekins or soup crocks. Top each with the mac and cheese. Sprinkle with remaining gruyere and panko. Place on a baking sheet and broil on high until the cheese has melted and the tops are golden brown, about 2-3 minutes. Serve warm and enjoy!