An Invoice can also be Mark as Paid from within the single invoice view.
Selecting Yes from the slider under Mark as Paid:
The options for the Payment Account the account the payment is to be published to appear underneath. Simply select the relevant accounts from the drop down menus. If the default Payment Methods have been set under company Supplier Settings, these defaults will appear. They can be edited in in the single invoice view if required. The remember me function will ask if these selections are to be remembered for future invoices.
The amount defaults to the invoice gross total, payment date to the date of the invoice and reference to the invoice number (if present). These fields can be edited if required. If edited, the blue return arrow appears to the right allowing a quick reset to the invoice defaults.
Specific Requirement for Quick Books Online:
QBO requires an extra payment method selected which appears below the reference field.