Invoicing retainers
You can choose to display retainer category entries and/or items applied to a retainer on invoices. An invoice reflects the total of all retainer category entries, plus the total of all items not applied to the retainer. Items applied to a retainer do not lower the total for the invoice. You can include a retainer total and balance by checking the appropriate checkbox when creating an invoice.

Be sure to review the information on reporting retainers, which also applies to invoices.