I hold complete sets in the smaller 4-pocket pages but this works with nine-pocket as well. It is organized as a book as follows.
"Cover" (first page with no opposing page) has the four different booster packs displayed.
Once you open that page, the left side has foils 1,2,3,4 and the right side has the regular 1,2,3,4. This repeats to the end. So each page flip shows four more cards, both foil and regular.
The cards without alternates are always numericially at the end, and just go there. Seems to work well.
All other cards, Stamped, DPxx promos, etc are stored in another smaller binder on their own. With the exception of the foil versions of piplup, chimchar and turtwig with regular card numbers on them, for some reason they are in the DP binder.
And the reason for the 4-pocket pages is simple, the binders come with zippers and keep the cards from falling out, and they fit in my son's backpack easier.