Melt the butter in a large skillet over medium-high heat. Whisk in the flour and cook for about 1 minute, stirring constantly to make a rue. Whisk the milk into the butter and flour mixture. Continue to whisk, and cook until the mixture is smooth. Stir in the 4 cups of the cheese and continue to stir to melt the cheese. Season with salt and pepper. Fold in the cooked macaroni and the thyme and fold to coat the macaroni with the cheese mixture. Pour into a 9×13 baking dish and top with the remaining 1 1/2 cups cheese. Bake for 30 minutes, until hot and bubbly.
While that bakes, saute the bacon until crispy. Add onion and cook for about 5 minutes to soften the onion. Before serving top the macaroni with the bacon & onion mixture.
Recipe heavily adapted from Tyler Florence