Really, how you organize your cards is completely and entirely up to you.
The most common methods of organizing cards that I've seen are are:
Pokedex: Organizing them by national pokedex number, in order to have 1 copy of every single pokemon.
Preference: Based on how much you as a collector like the card. Your favorite cards rise to the top, where your least favorites sit at the bottom or are cast off to the side.
Rarity: Your Secret rares(Primes, ex, legends, etc.) go in front, followed by shinies, followed by holos, followed by stars, followed by uncommons, followed by uncommons, and etc.
Artist: You put your collection of your favorite card artists up front,.
Play Value: your most competitively playable cards go up front, with everything else after
Set: You organize your cards and divide them by set numbers, and leave spaces for cards missing from your collection.
Type: Pokemon, Trainers, Supporters, Energies are all separated into distinctive sections for quick access.