I've made a few changes to my card storage, namely in terms of sleeves. Instead of the penny sleeves I kept all cards in before, I now stick all cards in at least a KMC Perfect Fit sleeve. RHs, holos, ultra rares, special cards I'm collecting (like the Eeveelutions, Zorua, and Mew), etc then all go in a KMC black Hyper Mat sleeve as well (with the inner sleeve upside down sealing the card in) That then either goes in an Ultra Pro Pro binder or a toploader in a toploader binder. The Ultra Pro Pro binder has my Plasma Freeze, Plasma Blast, Legendary Treasures, Radiant collection, and Kalos Starter Set collections (plus some other random cards to fill space) sorted by number though minus the ultra rares from them, with RHs replacing the normal or holo card as I get them. Then there's the toploader binder for the Pokemon I'm collecting, holos that I've swapped out with RH from the set binder, ultra rares, and so on.
Here's a rather large picture from that binder (albeit with one card out of place). I really like how the toploader cards look in the black-backed sleeves, makes it look more professional!