Many companies require a deposit from a customer, which is later applied to the customer’s charges.

In the Invoice Wizard, select Create a DEPOSIT - MANUAL invoice and create the invoice for a set amount.

When the customer pays the deposit, select Deposit Payment in the Payment Wizard.  The deposit payment will be applied to the deposit invoice, but it will also be stored as a payment that can be applied to future invoices.

Create an automatic invoice for the final charges in whatever manner you choose.  You can then apply the Deposit Payment as a credit to the invoice.