From the order list screen in your Order Management System (OMS), click on the order number of the order you wish to modify. This will take you to the order detail screen.
Here you will see the Edit and Add buttons next to "Line Items". Use the Add button to add an item you wish to put in the order.
Use the Edit button next to Line Items if you wish to edit quantities, recalculate the unit price, change the sales tax rate, manage the application of coupons, gift certificates, or loyalty points on the order, change the shipping on an order, manage affiliate attribution, and more.
To delete items, click the red X to the left of the line item you wish to delete. Note these red X's will only appear when there are multiple items in an order - they will not appear when there is a single item in an order, because there must always be at least one line item in an order. (So, if you are replacing all the line items in an order you must add the new items before deleting those that are being replaced.)
Then process the order as normal.
Please note that changes to the order do not automatically make changes to any credit card processing that has already been done. If you've already charged the credit card and are now modifying the order resulting in a changed total for any reason, you will then have to do the necessary credit card processing as well to refund a partial amount or charge an additional amount, as required. This is accomplished in the credit card terminal accessed by the blue "credit card terminal" button at the bottom of the order detail screen.