Separate by purpose
Start with four groups: personal collection, deck cards, trade or sale cards, and bulk. This makes every later step easier.
Sort by game and set
Keep each game separate. Within each game, sort by set, card number, rarity, or color/type depending on how you use the cards.
Protect valuable cards first
Cards with meaningful value should be sleeved and stored separately from bulk. Keep a simple inventory with card name, set, condition, and estimated value.
Use labels
Labels turn boxes into a usable system. Label by game, set, format, deck, or trade status so you do not need to open every box to find one card.
Review regularly
Collections change. Review your trade box and value cards every few months so outdated prices and forgotten cards do not pile up.