Currently I have the Pt series and the BW series sets spread across 4 different 1.5 inch binders, and am planning to continue with XY, then backtrack through the DP block, and then again from the Neo sets to Base set. On the side of each binder, I put abbreviations of the sets contained within, and I print out the logos for each of the sets to put in the front cover sleeve. Inside I have Ultra Pro 9-Pocket top loading pages for the (generally) four sets. My EXs, SRs, etc. are each in a blue Ultra Pro sleeve in their respective pocket in accordance with set number, though I intend to soon expand this to my Reverses and eventually to all of my collection, due to the massive amounts of dog fur that accumulates in my house. Older Promos are kept in pages right now in another binder that is an entirely different colour, while the current promo series (XY) are in an old 4-pocket DP era portfolio.
My bulk commons, uncommons, and regular rares are stored in cardboard boxes designed to hold trading cards, organized by set and number. Bulk reverses and holos are kept in cheap sleeves (about 5-15 per sleeve), as well as extra deck staples that I have no need for but can trade away at PRs. Extra Dragon Vault and Radiant Collection cards are placed in an old plastic Moltres Deck box. Energies are Putin old coffee containers according to type, and fit quite nicely. Bulk EXs And SRs are in with my XY promos.