If you need to manually add an order, you can do so by going to the Orders screen within your Shop Portal. (You can also click here)

You can scroll down until you see the button labeled "+ Manually Add Order". Click on the button.

Here you can choose the affiliate to associate the order to, whether it was a Referral URL or Discount Code sale, Order number, sub-total, commission rate, referral code (if applicable) and order date.  Be sure to click SAVE when finished.  The order will immediately show up in the orders screen.