Stir in the flour and cook for 1-2 minutes. Gradually whisk in the milk, stirring constantly. Add the garlic powder, salt, and pepper, and stir until the sauce thickens.
Remove from heat and mix in the cheddar and Monterey Jack cheeses until melted and smooth.
Begin by placing a third of the potato slices at the bottom of the Crock-Pot, followed by a sprinkle of a third of the chopped onion. Top this layer with a third of the cheese sauce.