Refunding customers that have made purchases through Checkout X actually happens in the same way like making purchases through the Shopify checkout.
Step 1: Open your store in Shopify and go to Orders > All orders.
There you will find all of your orders and you will need to select the one that you want to refund.
Step 2: When you open the order that you want to make a refund of, click on Refund.
Step 3: Then, choose the quantity of the product that you want to refund. You could also add a reason for refund in the field below. At the end, just click on the Refund button on the right side.