I kind of have a weird heap/stack system when it comes to organizing boxes. That has been pretty useful in gen 6, as I was particularly active during this generation, especially in terms of Pokedex completion and breeding for competitive Pokemon.
The basic layout looks like follows:
- the first box is empty, unless I want to trade some Pokemon via manual trading, which is when I move the ones I want to trade to said box (prevents me from scrolling through all the boxes after every successful trade)
- from box two onward every Pokemon that doesn't solve a purpose besides filling my Pokedex, gets sorted by its primary type (except legendaries)
- after those come the boxes containing legendaries
- the last box contains all my Pokemon that serve a certain purpose ingame (ingame teams, Pokemon catcher, Pickup squad, etc.)
- the boxes before the job-box contain my "elite", basically all the competitive Pokemon I have
- before those comes the breeding section (future breeding projects, Dittos/Synchronizers, positive breeding leftovers (additional mons with all around perfect nature and IVs that I don't need for the moment))
- every other box between legendaries and breeding mons is empty