Preheat over to 350 degrees. spray 8- 1 cup baking dishes with nonstick spray, place on a baking sheet.
Melt 2 tbsp butter in a large saucepan over medium heat. Add onion; cook, stirring, until softened, 4-5 minutes. Add flour and cook, stirring 1 minute. Gradually whisk in milk. Increase heat; cook, whisking until slightly thickened, 3-4 minutes. Add cheeses, salt, and pepper; cook, whisking until cheeses melt.
Remove from heat; stir in macaroni. Divide among baking dishes. Melt remaining butter in a small nonstick skillet. Add the bread crumbs and cook, stirring constantly, until they are evenly coated, about 1 minute. Sprinkle over macaroni and bake until bubbly and the tops are golden, about 25 minutes.