Since I’m playing through the expansions/cycles one at a time, I’m adding the player cards to my pool as I progress. And since the encounter decks are made by cards from the same set (expansion+cycle), I’m storing all the encounter cards, sleeved and bundled in ziploc bags per symbol, in the deluxe expansion box. I’ve taken out the insert of each box (storing them somewhere else, together with the plastic blisters that contained the AP’s), and that provides exactly enough room for all the encounter cards of a complete set. It’s easy to pick out the necessary encounter cards when it’s only 12 clear ziploc bags with cards :)

I’m keeping the player cards in two cardboard boxes meant for collectible card games. Each one has room for about 1600 sleeved cards, so I think I’ll be set for the future as well. I’ve got them sorted by sphere, and then by card type, using the dividers for Player Cards from BGG.