Select the invoice you want to apply a payment to and enter the amount. In the 'received from' field, input the customer’s name. How to Apply Customer’s Payment to Invoice CorrectlyĮnter your QuickBooks and click on customers then choose to receive payments from the options. Below is a detailed step of the processes you need to follow. You will see how to handle payments and invoice in your QuickBooks in this article. QuickBooks allows you to take record of all your account income and expenditure, organize your records and track time.