QuickBooks Tip
(From QuickBooks Knowledge Base)

Receiving a down payment and later applying it to an invoice

From the Activities menu, select Receive Payments, and then fill in the Customer Payment window as usual.

When you're recording a down payment, and you are doing more than one job for the customer, be sure to specify both the customer name and the job name in the Customer:Job field. This ensures that QuickBooks will apply the down payment to invoices for the correct job.

The entire payment amount is displayed in the Unapplied Amount field. QuickBooks holds the unapplied amount with this customer's name so that when you do have an invoice for this customer, you can apply the down payment amount.

(Optional) Click Print Cred Memo to give the customer a receipt for the down payment.
The credit memo is for your customer only. It does not become part of your financial records in QuickBooks, only the payment will show as the credit.

Click OK.
When the invoice is created, link it to the down payment already received:

In Receive Payments, select the Apply Existing Credits checkbox to apply the credit amount to the invoice.