When an invoice is manually created from the order, click 'Submit Invoice' button to process the invoice and capture the sale. At the bottom of the invoice page you have 3 options, these are:
When the invoice is submitted, the system captures the payment from the third-party payment gateway. You have the ability to create a credit memo and void the invoice.
When the invoice is submitted, the system does not capture the payment. It is assumed that the payment is captured directly through the gateway, and you no longer have the option to capture this payment through the system. You have the ability to create a credit memo, but you do not have the option to void the invoice. (Even though the order used an online payment, the invoice is essentially an offline invoice.)
When the invoice is submitted, the system does not capture the payment. It is assumed that you will capture the payment through another means. There is a Capture button in the completed invoice. Before capturing, you are able to cancel the invoice. After capturing you are able to create a credit memo and void the invoice.
Do not select 'Not Capture' unless you are certain that you are going to capture the payment through store at a later date. You will not be able to create a credit memo until the payment has been captured using the Capture button.