So, in my au the boxes are all completely different.
The first layer kwamis are in their respective pairing and in separate boxes as seen above. Each pairing has a name for what they represent:
Ladybug+Black Cat- Matter duo
White Lion+Hellhound- Energy duo
Caladrius+Bat- Conciousness duo
Unicorn+Stick Bug- Existence duo (thanks @hades-999 for the idea!)
The pairs were kept in one of the 4 (technically 5) temples. They were barely mixing and a pair was always released together. The Guardians believed if they didn't the universe will be unbalanced.
The other boxes usually had a second layer kwami who was in charge/above the others. I'm gonna call them alpha for now. They were mostly like this
Peacock of Emotion (alpha)
Dolphin of Intercommunication
Sense box (mostly just Vision)
Fox/Kitsune? of Illussion (alpha)
Scorpion of Hallucination
Butterfly of Transmission (alpha)
Snake of Repetition (alpha)
Bison of Vibration (alpha)
Salamander of Magnetization
Dragonfly of Motion (alpha)
Jellyfish of Transparency
Penguin of Temperature (alpha)
Thunderbird of Electrification
Now, these weren't like this most of the time. It honestly depends on who was in charge of the box arrangements at that time. For example, the Snow Leopard was constantly being moved from the Timekeeper box to the Elemental box, and the Consciousness duo was in the Emotion box before they separated the duos.