If you need to refund or surcharge more than one order at a time, you can filter for the orders, and select all, or just the orders you need to modify the charge on. Then scroll to the bottom of the Orders page, and hit "Bulk card charge/refund".
Click "Add row" and under Fee note add the Description or reason for the charge, ie, "Shipping overcharge" or "Bottle refund". In Value enter the amount, either a positive or negative value, with NO $ dollar sign. Click the Update button.  
You will see a list of the orders updated. Click to view the order and you will see the new line item added on the order.
There is no way using bulk update to charge the actual shipping rate, you need to charge a flat fee, if you do it that way, OR do each one manually to charge the actual shipping rate. To modify the order and charge the actual shipping rate, use the Customize Order button and switch it from Hold for Pickup to Ship. After you save, it will show you the amount to surcharge. Hit Surcharge.
NOTE: Your customer will receive an order update notification including the new line item.

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