When you have received payment from your client, its time to mark the invoice as paid. This can be done either directly from the bank import or from the Invoice Summary page.
From the 'Work > Invoicing' tab.
Click the options button next to the invoice that you want to pay and choose Pay Invoice.
The system will automatically populate the Payment Date, Amount Paid, Ref and Bank Account used. You can manually update as required and add the Payment Type if required. Click Make Payment to pay the invoice.