Just as you can link a payment receipt to an invoice through the QuickBooks desktop user interface, you can establish this link when importing customer payments into QuickBooks using Zed Axis. There are two ways you can do this:
Auto Apply Payments
In the same way you can click the Auto Apply Payment in the QuickBooks user interface (QuickBooks automatically applies a customers payment to the outstanding invoices for that customer. If the amount received is less than the customers outstanding balance, QuickBooks applies the payment to the oldest invoices first).You have the option to select this option when importing receive payments into QuickBooks and the same behaviour will be applied. When setting up the mapping in Axis ensure that you map the "IsAutoApply" and set this to true, if the field is set as false the payment will not be applied to any invoices and will just appear as a credit on the customers account.
Applying to a specific invoice or invoices.
You can apply the payment to specific invoice during the import. You will need to map the field ApplyToInvoiceRef to specify the invoice that the payment is to be applied to and provide the Invoice Reference Number (InvoiceRefNumber) that you wish the payment to apply to and the Payment Amount. If one payment is being applied to multiple invoices then you will need to have a row for each invoice that is being paid and set a common Receive Payment RefNumber to group them together.