Melt 2 tablespoons butter in a large skillet over medium-high heat. Add the onion, thyme, onion powder and a pinch of salt and pepper to the skillet and cook, stirring occasionally, until the onions soften and brown, 3 to 4 minutes. Remove the onions to a bowl and leave the skillet on low heat.
Place one slice of Cheddar and one slice of Swiss on each piece of bread. Top 3 of the slices with the onion mixture, then sandwich with the other cheesed breads, making 3 sandwiches. Spread about 2 tablespoons butter on the tops of the sandwiches, just enough to cover the tops in a thin layer. Melt the remaining 2 tablespoons in the skillet (adding more if it looks dry). Place the sandwiches butter-side up in the skillet. Cook on one side until golden brown, 2 to 3 minutes, then flip and cook the buttered side for another 1 to 2 minutes. Remove from the skillet and cut crosswise into strips—great for dipping in soup! Serve immediately or keep in a warm oven in aluminum foil until ready to use.