Invoices remain in an open state until the balance is cleared either by recording payments or applying open credit notes to the invoice balance. This page describes creating and managing payments (where a customer has actually paid you money). Creating credit notes and applying them to invoices is covered here.
To record a payment against an invoice click the " Payment" button on the relevant invoice or click the " icon on the payments list to the right of the sale workflow page.
Enter the cash amount paid, optional reference and date of payment.
Applied payments are listed at the conclusion of the invoice on screen and also on the invoice PDF (if regenerated):
When creating a payment, if a value greater than the outstanding balance is entered, then the invoice will be marked as fully paid and an "overpayment" will be created. After creation, overpayments act identically to credit notes. They represent a credit to the customer's account and their value can be applied to future invoices.
After creating an overpayment, if you wish to undo the whole operation, you'll need to delete both the invoice payment and the overpayment from the sale.