>>16711093pretty much this. I used to try to do it by type, but that got way to annoying, plus types aren't evenly spread, and dual types would screw with me.
Now I have a 4-5IV M, 4-5IVF box, a Legendaries, a box for my 'travel' pokes (HM, assorted Synchro natures, the team I use to clear Le Wow, etc.) and a box or two to save rejects, everything else is just a clutter.