I organize them all alphabetically. It's much easier for me to find cards that way, as opposed to organization by set, by type, or by Pokédex number (which was how I did it at the beginning). There's a very complicated way for me to organize them after that, though. You probably don't need to do it that intricately.
As I sleeve ALL of my cards, I can't use rubber bands, or else they'll ruin the sleeves. I just have them loosely stacked with cardboard pieces separating them within a small group of boxes.