How to Mark Invoices as Paid
When your customer pays you by clicking on the pay now button directly from the invoice you sent them, the invoice is automatically marked as paid as soon as the payment is made.
When you manually enter a payment for your customer, either by connecting your Square account and charging their credit card or by entering a manual payment such as a mailed check the invoice is marked as paid. This is a great way to keep track of possible missing payments. If someone is mailing you a check, add an invoice and mark it paid when you receive it. You can check your invoice list weekly to make sure nothing has fallen through the cracks.