Side decking is a critical part of a match. It can determine the outcome of game 2 and 3. Let's have a look to a proper way of siding. All have to be done beforehand.
There is no way to make no mistakes if you are trying to figure out what to take out/put in right there on the spot. The cards in your side deck should be pre-
determined about what they will replace. Let's look at every step separately.
Step 1: Determine the competition [List A]
Make a list of the decks you are about to face, and which decks your own deck has a problem against. There are certain decks that work well against others, and some
that don't work at all. When you're done you will have a list of all the decks you have trouble with.
Step 2: Take out the useless [Lists B, C, D...]
Check your main deck, and see which cards from your main deck are completely useless against each one of them (the decks from the List A). Those are the cards that
will need to be taken out when you side for each one of those decks. In the end you will have created some lists, equal to the number of decks you have trouble
facing. If for example you already determined that your deck has trouble against 3 different decks, in this step 3 lists will be formed.
Step 3: Counter Strategy [Lists E, F, G...]
Since you have already determined which cards need to be taken out for each "troublesome" deck, now you need to determine which cards are to be put in their place.
Again, work separately for each deck, and fine cards that work especially well against that deck. Each deck once again will have its own list.
Note: Since the side deck provides limited space (15 cards max) you need to be "smart" during this step. Find cards that work especially well against multiple decks
in your list, so that you save up side-deck space, and use it for other, more "specific" cards.
Note 2: In this step you should be careful not to "ruin" your own deck in the process. Each deck functions in a specific way, and its main "body" helps to achieve
just that. Changing cards will inevitably throw it off balance, you can only try to minimize the damage by not taking out "key" components. Even if a card doesn't
work especially well against a certain deck, if it one of the main cogs of your deck, and you cannot do without it you shouldn't take it out. Similarly, if a card you
chose for your side deck works especially well against one of your "troublesome opponents" but in the meantime it totally disrupts your own plays and strategies,
shouldn't be included at all.
Step 4: Mutual Changes
Now that you are more focused on what cards you are going to use, go back to step 2. Take those lists and the lists from step 3, and "assign" each card from the step
3 lists to a card from the step 2 lists. This way you will specifically know which card to take out from your main deck for each card in your side deck. No more
confusions between games and no more swapping mistakes in the side-decking process.
Note: That particular step can be wrote onto a piece of paper and be kept with the deck in case you have to side against a deck. Then by having a quick look you will
be sure you will side the right cards, for the right counter options.
Step 5: Too obvious dangers
The fact that you side, doesn't mean your opponent won't. If there are certain cards that hurt your deck in any way, you can be almost certain that your opponent will
side them against you. This is another thing you should be careful during steps 2 and 3. Find solutions (and embed them in your side deck if possible) for cards that
your opponent might side against you, that will have a negative impact on your deck.
Step 6: First or Second???
Going first or second in game 2-3 alters the way you side for the next duel. Siding some traps for game #2 when you won the fist and you're going second now is not
such a good idea. Your opponent will have the fist turn available to set up his/her field and probably not let your trap cards even resolve. Going second in game 2-3
indicates the need to side more "direct" cards like Spells and Hand-traps (Effect Veiler etc) assuming that your opponent will make his/her moves in his first turn, and the
only way to stop him or disrupt his strategy in the second round is by playing Spells or Hand traps. Also, some decks pull off "locking" combos in the first turn,
making your trap cards all the more difficult to be activated and resolved properly.
When you lost the first duel then it means you will go first in the second one. You will have 1 "free" turn to set up your field for your opponent, and now you can
easily side those trap cards, because in case you draw into them they will be set without trouble. This time you have more possibilities to control the game instead
of your opponent, so try to do just that.
Subject: Methodology of Side Decking 
