Melt the 3 tablespoons butter in a skillet, add the onions and 1/2 teaspoon salt, and cook over medium-low heat for 35 to 40 minutes until deep golden.
Boil the cavatappi in water with 1 teaspoon of the remaining salt for 3 minutes less than the package directs and drain.
Melt the remaining butter, whisk in the flour, then gradually whisk in both milks, Worcestershire, pepper and the final 1/2 teaspoon salt until thickened.
Combine the pasta, sauce and onions in a buttered 6-quart crockpot and cook on low for 45 minutes.
Stir in both cheeses by handfuls and cook for 30 to 45 minutes more until smooth and tender.