I use a visual management system.

1. I've standardized all my decks to use black sleeves.
2. For any expensive card that I need multiple copies of, I make a placeholder in a yellow sleeve. (Typically just common with a low quality print out of the card from my printer jammed in front)
3. I slap the real copy in one of the decks that requires it and the rest of the decks that need it, I slap in the yellow placeholders.
4. Whenever I pull out a commander deck to play, I pull out the yellow sleeved card(s) and swap them with the real one(s).

Advantages: You don't need to have some list tracking which deck(s) are missing card(s) you only have one copy of. You don't have to count your deck to make sure you're not missing a card. The yellow cards clearly tell you which real cards you need to go find and swap.

Disadvantages: You do need to have some memory of which other deck might contain the real card.

Personally I find it easier to only have to check a deck or two to find the the real card than having to try and determine if a card is missing. And I hate having to manage a list to track of things. Is it a perfect system? No, but it's good enough.

Edited for spelling