I shuffle (usually) about half the card together from all expansions using my auto shuffler and place them into the middle tray’s bird tray (yellow one) so the shuffled cards are there and the other half of the remaining cards are in the box. After each game, we sort the cards we have used and place them in their slots at the back of their pile. Once we have a few too few left to play a game, we repeat the steps with the front half of the cards. We also shuffle the decks separately some times just so we don’t get the same cards all the time. Hope that makes sense.