TL;DR and Video Guide at the bottom of the page.
The first thing that you will need before making an order is your PTCGO screen name. You can find your screen name by going to the official pokemon.com website and logging in, then select Pokemon TCG Online settings under edit profile. You will need to input your screen name during the checkout process so that a friend request can be sent to you to send you your order.
While you are still logged into the pokemon.com website, stay in the Pokemon TCG Online settings and make sure your social preferences are set to "Open". This will ensure that trading is fully unlocked on your account as your order is sent to you via private trade.
You need to have a tradable pokemon item available, it is recommended that you set an unneeded common or energy card "for trade".
To identify which cards are tradable and which are trade locked, refer to the images below.
Be sure to let us know which card you want us to trade for if you have multiple cards set to "for trade".
If you don't have a tradable card, you can purchase the Pikachu avatar set and set it to "for trade" the same way. To obtain it, click on the Shop button when in game and select Shop, then select the gameplay tab and the first item available for tokens is the Pikachu avatar set. The video below shows the process of obtaining the Pikachu avatar set.
To set a card to be tagged as "for trade", go to the 'Cards' button on the top left of the screen, select 'Collection', then scroll through a card you don't need, like a common or energy card, and click on the button to the right of the card that has 2 arrows pointing away from each other, if it's highlighted in orange, it is tagged as "for trade", shown in the image below.
Once you have completed your order. A friend request will be sent to you with the screen name that you input during checkout. Please accept the friend request. After the friend request is accepted, a private trade will be sent to you with your purchased card(s)/pack(s).
To accept a private trade offer, click on the "Cards" button at the top of the screen, then click the "Trade" button, and finally select the "Offers to Me" tab. Then double click on the trade offer, and just hit accept. And that's it!
TL;DR:
1. Enter your screen name during checkout.
2. Set-up a tradable card. Enter which card you want your order sent for at checkout.
3. Accept the friend request once it is sent to you.
4. A private trade offer will be sent to you for the card you set in step 2.
5. Accept the trade offer!