When you capture an order, you confirm that the order has been fulfilled. This means that you’ve shipped the ordered goods to your customer. At the same time, it lets us know that we should trigger a payout to you, and charge the customer for the order amount.
You should always capture your orders manually in your e-commerce platform. Only if you are experiencing an issue with your e-commerce platform, you can be done on the Order section of the Merchant Portal as well. This is because when you capture an order on your e-commerce platform, will also reflect on the Merchant Portal and update the information there, but not the opposite.