There are two methods to record this payment,
Retainer Invoices: Under the Sales module, click on Retainer Invoices and select + New. Enter the details of the customer, Description and the Invoice Amount. Click on Save or Save and Send as per your preference. Once the payment is recorded for the retainer, you can apply this retainer towards the invoice created for the purchase.
Payments Received: Under the Sales module, click on Payments Received and select + New. Select the customer from the drop-down and enter the Amount. This amount will be saved as unused credits that can be applied to an invoice for this customer. If an invoice has already been created, you can also enter the amount under Payment against the invoice.