Sometimes, to keep track of what's where easier, even though I mostly always return the Pokémon to the spot in the box that I took it from. I currently have a "Gigantamax 1" and an "Isle of Armor 1" box.
The thing about boxes for me is the wallpapers. Back in the good old days of gens 3, 4 and 5, the default setting for wallpapers was a loop of all the basic wallpapers available - the woodland one, the mountain one, the cave one, the sea one... My sister and I arranged our Pokémon by habitat using the wallpapers, and you always knew where everyone was (down to the exact place within the box - you put it back where you took it).
In Shield, all boxes have a blank wallpaper by default, so putting wallpapers on all of them and rearranging my Pokémon to be in properly-themed boxes will take a bit of work, but I'm hoping to do just that in the coming days. I just really like it that way.