To remove a payment from an invoice, go to the Sales tab on the left pane and then click Payments.
Click the Job Number associated with the Invoice you want to delete.
Once in the Invoice tab, you can either delete the invoice by clicking the drop down menu next to the invoice number or go directly to the invoice by clicking the invoice number and scroll down.
Locate the payment and Select 'Delete'.
Confirm your Action, Select 'Delete'.
Depending on the action the Balance of the Invoice will adjust by the payment amount reversed.
If the payment was taken by eWay you can refer to the Help document here.