Place brats and sliced onions in a two gallon zip top bag. Pour the beer into the bag, remove as much air as possible and seal the bag. Place the bag in a bowl and then into the refrigerator for at least 6 hours, but overnight if possible.
Remove the brats from the refrigerator and place on the counter while you preheat the grill. Light your grill and set up for two zone cooking. Add an optional chunk of pecan wood for added smoke flavor. Close the lid and establish temperature in the grill at 375°F.
Remove the onions and brats from the bag and place them into a large cast iron skillet. Add half of the beer from the bag to the skillet.
Place the skillet on the grill over indirect heat. Close the lid and allow the brats to boil in the beer for 30 minutes.
Remove the brats from the beer and set aside. Move the skillet over direct heat. Add the butter and brown sugar to the onions, and cook until the liquid cooks off and the onions turn dark in color. Add in the thyme and combine; move pan to indirect heat.
Place the smoked brats on the grill grates over direct heat and sear the outside. Flip them often to ensure they don’t burn, for a total of about five minutes.Remove the onions and brats from the grill. Place the brats in the buns and top with onions, or other toppings of choice.