How do I create a retainer invoice and apply the retainer received toward an invoice?
In the Retainer screen, you can click on the Request Retainer button. You need to enter the client and project (optional), retainer amount needed and then process this request. This creates and sends out the retainer invoice to the client.
When the client pays you the retainer, go to the Payments screen and enter that payment by selecting 'Apply as retainer'. This is the retainer received and available from the client.
You can then use this available retainer in the Invoices screen while creating an invoice or apply it later on an invoice in the Payments screen (Use Retainer pay method). Check the Core Help for details.