Follow these detailed instructions to create the most delicious and comforting cheesy scalloped potatoes every time:

1. Prepare the Potatoes and Onions: Begin by peeling the russet potatoes. Once peeled, slice them thinly, about 1/8 inch thick. You can use a mandoline for uniform slices, or a sharp knife. If using a knife, aim for even thickness to ensure they cook evenly. Place the potato slices in a bowl of cold water to prevent them from browning and to remove excess starch. This step contributes to a creamier texture in the final dish. Next, peel and thinly slice the yellow onion. Mince the garlic cloves and set aside.
2. Sauté Aromatics and Make the Roux: In a large, oven-safe skillet (cast iron works wonderfully) or a large saucepan over medium heat, melt the butter. Add the sliced onions and sauté until they are softened and translucent, about 5-7 minutes. Do not brown them; you just want them to become tender and release their sweetness. Add the minced garlic and cook for another minute until fragrant, being careful not to burn it.
3. Create the Cream Sauce: Sprinkle the all-purpose flour over the sautéed onions and garlic. Cook for 1-2 minutes, stirring constantly with a whisk, to create a roux. This step is essential for thickening the sauce and preventing lumps. Gradually whisk in the milk, ensuring it is fully incorporated and the roux is smooth. Then, slowly pour in the heavy cream while continuing to whisk constantly. Bring the mixture to a gentle simmer over medium-low heat, stirring occasionally.
4. Infuse Flavor and Season: Add the fresh thyme sprigs to the cream sauce. Season generously with salt and black pepper. Remember to taste and adjust seasoning as needed; potatoes can absorb a lot of salt. Add a pinch of nutmeg to the sauce for a subtle warmth and complexity. Continue to simmer the sauce for about 5-7 minutes, stirring occasionally, until it slightly thickens. Remove the thyme sprigs before proceeding.
5. Assemble the Scalloped Potatoes: Preheat your oven to 375°F (190°C). Grease a 9×13 inch baking dish with butter. Drain the potato slices thoroughly and pat them dry with paper towels. This is important to prevent excess moisture in the dish. Arrange a layer of potato slices in the bottom of the prepared baking dish, slightly overlapping them. Sprinkle a layer of shredded cheddar and Gruyere cheese (if using) over the potatoes. Repeat layering potatoes and cheese until all potatoes are used, ending with a layer of cheese on top.
6. Pour Sauce and Bake: Pour the warm cream sauce evenly over the layered potatoes and cheese, ensuring all potatoes are submerged in the sauce. Gently press down on the potatoes with a spatula to ensure they are fully immersed in the sauce. Sprinkle the grated Parmesan cheese evenly over the top.
7. Bake to Golden Perfection: Cover the baking dish tightly with aluminum foil. This will help the potatoes cook through evenly and prevent the cheese from browning too quickly. Bake in the preheated oven for 45 minutes. After 45 minutes, remove the foil and continue to bake for another 20-30 minutes, or until the potatoes are tender when pierced with a fork and the top is golden brown and bubbly. The baking time may vary slightly depending on your oven and the thickness of your potato slices.
8. Rest and Serve: Once baked, remove the scalloped potatoes from the oven and let them rest for 10-15 minutes before serving. This allows the sauce to thicken slightly and the flavors to meld together beautifully. Garnish with fresh thyme sprigs (optional) and serve hot. Enjoy your incredibly cheesy and comforting scalloped potatoes!