Cook macaroni in a large pot of salted water until al dente.
Meanwhile, melt butter in a large saucepan over medium heat. Whisk in the flour, cook for 1 minute to eliminate the raw flour taste, then reduce heat to medium-low.
Slowly pour in your milk, whisking continuously to make sure the mixture is smooth. Simmer slowly until mixture begins to thicken. Season with salt and pepper.
Turn heat to low. Add cheeses, one handful at a time, whisking until cheeses are fully melted and incorporated before adding the next handful.
Drain pasta and stir into sauce. If mixture is too thick after adding pasta, add more milk, 2 T at a time, until desired consistency is reached. Mixture will continue to thicken as it stands and cools.