How to organize a Pokémon card collection
Sort by set first, then by collector number within each set. That mirrors how cards are catalogued everywhere else, so any card can be found by the number printed on it rather than by memory.
Sort by set, then by number
Alphabetical sorting by Pokémon name breaks down immediately, because the same Pokémon appears across dozens of sets. Set and number is unambiguous, and it matches how binders, price guides and marketplaces are organised.
Keep valuable cards separate from bulk. Sleeving everything is expensive and unnecessary; sleeve the cards worth more than the sleeve.
Split the digital list the way you split the physical one
Separate collections for vintage, modern and cards you intend to sell make totals meaningful. One combined list tells you a number but not which part of the collection moved.
Trade stock is worth its own collection. Knowing the total value of what you are willing to part with makes trades much faster to evaluate.
Questions
Binders or boxes?
Binders for cards you want to look at and cards worth protecting, boxes for bulk. Use side-loading binder pages, since top-loading pages let cards slip out when a binder is tipped.
How should I store cards long term?
Upright, out of sunlight, somewhere stable and dry. Heat and humidity warp cards, and a warped card loses value even if the surface is perfect.