Does anyone have advice on how to handle a 50% deposit for a customer without invoicing until the end of the job?

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

I have often done this: create a deposit account and then create an invoice for the deposit amount and apply the payment to that. At completion of the project I typically create a final invoice and then apply the deposit payment to that and delete the original invoice. You have to remember to back date the final invoice to BEFORE the original deposit payment though - or it shows as unapplied....complicated.