You control what you need and how you are doing it, but there are Reasons to do it like this: "One to collect a deposit and a 2nd to collect final payment. WHY can I not consolidate everything under one invoice per customer?"
Example:
I am going to install your new carpeting and require 50% up front; you are Not paying for half the installation or half the carpet now. I am charging you a Prepayment or Deposit. That's the item I list on the first invoice or use on a Sales Receipt.
Then, later, I bring the new carpet and install it. I charge you this invoice in Full. I also make a credit memo for your Prepayment item and apply this to the Gross Invoice, the Actual Sale, to show it is partially paid, already.
And the Date of the invoice or sales receipt is the date of the sale. Also, if you are subject to Sales Taxes, that's why all of this matters. And if that carpet is in inventory, and I charge you 50% of it as if that is the prepayment, that implies I just removed 50% of your carpet from my inventory, but if that is not the reality of the situation, that's why you do Not make it as one invoice.
Hope that helps.