You can just receive the payment and it creates a customer credit memo for that amount and you apply it when you issue invoice.

Better is use a Sales Receipt for an item you call Deposit on Job and have that item post to a current liability account you set up as Prepayments. Not income but you now owe the customer. Then when job is done create an invoice and add a line item for the prepayment deposit as a negative.  Make sure the prepay item is not taxable when you set it up