I had my shipping information setup incorrectly and the customer selected one that is not available. It says I still be charged $9.97 even though I manually processed the order with a different shipping method myself. How can I avoid the $9.97 being taken out?
You are charged when you purchase shipping when shipping item to customer. If you shipped using other service, you only pay for that shipping. (Ex. Customer pays $10, you use another shipping that costs $5; you only pay $5)