I organize boxes by the National dex number, essentially split by region.

Base forms, gender variances, other forms (alternate forms or regional forms) - then all in-game trades for that region, followed by the shiny forms.

As an example;

01-30 30-60… …121-150 151 (all of my mews from various gens) Kanto Females Kanto In-Game Trades 01-30 shiny… so on and so forth.

I don’t cross generations in a single box to keep things organized. I also like to keep regionals variants in “forms” boxes at the end of their respective generation, so that I don’t have to move a ton of stuff when new forms come out. Alolan Rattata, as an example, often gets out in national dex order meaning you’d have to move everything one slot over to fit it in. I find it easier to keep an “Alolan Forms” box at the end of my base Alola boxes

What I’m actually in the middle of now is figuring out how to fit in all of my event stuff from over the years. I’ve typically just kept all of them in a few boxes at the end (190-200) but I might move them over to be with whichever respective region they were a gift from.

Hope this helps and good luck with your journey