You have the ability to create Retainers and use these to record customers' deposits. For more information about the Retainers feature please see this article.

Posting Customer Pre-Payments/Deposits Without Using Retainers

To post a customer prepayment, payment or deposit:

• Go to the Sales command center and click Enter Sales.
• Select the customer, create a Service Invoice with the status of Invoice with a $0 amount. You can post this to any account since it will be a zero dollar amount. Enter information about deposit in the Description field.
• In the Paid Today field, indicate the full amount of the deposit.
• Enter the correct payment method in the Payment Method field, processing a credit card, if necessary.
• When you click Record to save, you will get the message, "This sale has very little information... ." Click OK.
• A Credit Memo will now be in the Sales Register, under the Returns & Credits tab. You can apply this credit memo to future invoices, or pay a refund to the customer.