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.
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 the up and down arrow key
Enter in an Apply Amount
Press Enter/ Return on your keyboard.
The Enter / Return key commits the applied payment amount to the selected invoice
Select Save 
If you have additional payments to apply for other deposits, click Yes when asked to apply more.
Otherwise, click No. 