Sales & Customers

I got an option for this in QuickBooks Desktop, shoshifein.

You can create a payment item and add it to the invoice. This will act as a partial payment which reduces the amount due, and this is visible to the invoice form.

1. From the Lists menu, choose Item List.
2. Right-click anywhere and select New.
3. In the TYPE drop-down lists, select Payment.
4. Enter the name of the item and select a payment method.
5. Click OK.

You can always go back to this thread if you have more questions about handling your customer's payments.