The second step in applying payments to Customer invoices is to use the Apply Payments function. A payment that reduces the amount remaining to be paid on a specific debit item, instead of merely reducing the total amount owed on the account.
Pre-Requisites
Access the Receivables module > Click Apply Payments
Use Filter criteria to find payment
Select a Payment from the Payment List for Company grid > Click OK
Select the Invoice you wish to apply the payment to using up and down arrow key
Enter in an Apply Amount> Press Enter/ Return on your keyboard.
The Enter / Return key commits the apply payment amount to the selected invoice > Save 
If you have additional payments to apply for other deposits, click Yes when asked to apply more. Otherwise, click No. 