Things You'll Need
Instructions
Buy several collector card sheets and a large 3-ring binder. These can hold your initial cards in a safe way while still allowing you to go through them to add and subtract cards from your deck. If the pages or binder fill up, get more. Don't try to over-stuff the ones you have.
Decide how many of each card you want to keep. Standard Rules say you can only have 3 of any one card in your deck and Tournament Rules cut down some cards to 1 or 2 per deck. While most people play with Standard Rules, it isn't uncommon to find people that don't play with Tournament; so 3 of each card is probably a safe bet.
Divide up your cards into piles of monster, spell and trap cards. You can then further break these sections down by type. Some people then break them down further, often alphabetically or by element (for monsters).
Place the cards in the book, giving each card its own line on the page. With standard collector card sheets each sheet has 3 columns of 3. With each card on its own line you can immediately know how many of each card you have. When you run out of a type of card, say equipment spells, start a new page, don't just continue with a new card type. Otherwise you can't add additional cards and sheets to their sections.
Separate your extra Yu-Gi-Oh cards to trade with your friends.