Name box 1 to "hacks from gts". all pokemon you get from trading will be stored either there or in your party (of course, you want to move these 'mons away to other boxes sometime...). otherwise, keep it empty.
Then store your pokemon in numerical order, naming the boxes 1-30, 31-60, 61-90 etc.... (formes of some pokes may need to be stored to another boxes.)
Why should you do this?
-searching for pokemons will be easier.
-checking what's missing from pokedex is easier.
-there is no way you could mess this up (imagine sorting pokes for types, what are you going to do with all 109 water types?)
-the main downside is that you have got a very limited room for other pokes like your teams, shinies or other cherished ones, but you can always put those together with normal ones in normal boxes.
i use my w1 game as a storage this way and my w2 for other business like masterarceus said earlier..
(once again i spent half an hour thinking to post or not to post.....)