As I collector, I've stored entire sets within plastic pocket-pages in 3-ring binders.
Extra current-format, "good" Trainer and Pokémon cards are stored in a plastic boxes, as well as, extra energy. Each group of cards is organized in alphabetical order.
I also carry 3 groups of extra, current-format cards (kept in plastic boxes) to all tournaments. These boxes contain extra energy, Pokémon and Trainers and are used for any last minute revisions to my tournament deck.
Lastly, any remaining bulk or overflow are stored in another box and most likely traded and/or sold.