I tend to sort my boxes by TCG color. I usually go by primary Type, but I may use the secondary Type if I need to make room (especially for the Blue and Green boxes) or to better-fill certain boxes (like Black or Gold).
Red: Fire
Orange: Fighting, Ground, Rock
Yellow: Electric
Green: Grass, Bug
Blue: Water, Ice
Purple: Psychic, Ghost, Poison
White: Normal, Flying
Black: Dark
Silver: Steel
Gold: Dragon
Pink: Fairy
Then I have separate boxes for Shinies.
SH Random: Full-odds and randomly-encountered Shinies post-Shiny Charm
SH Masuda: Shinies hatched via Masuda method
SH Radar/DexNav: Poké Radar and DexNav/Sneaking Shinies
SH Safari/Horde/Fish: Friend Safari, Horde, and chain-fishing Shinies