To apply one payment to multiple invoices in QuickBooks, select “Customers| Receive Payments” from the Menu Bar.
Repeat this until the total payment has been distributed to the correct invoices. To do this, place a checkmark in the checkmark column to the left of the invoices against which you want to apply the cumulative payment amount received. You can apply one payment to multiple invoices in QuickBooks for a single customer. Apply One Payment to Multiple Invoices in QuickBooks: Overview