You can create payments directory on the Invoice by clicking 'Mark Paid' or you can click Payments section in the left menu. It will take you to Payments screen where you will find a button that says 'Record Payment ' . Once you click that button, a dialog will appear asking you to type customer name to search. Start typing customer name and a list of suggestions will appear, you can select the right customer from the suggestions. Once customer is selected, it will ask you to choose payment method and Invoice across which payment is being created. When you are done with filling the required info, click submit and your payment record should be created successfully.