@ZackE Your response is insufficient and doesn't answer the original poster or anyone else's questions.

@DawnK @svieira  Hi, I am a bookkeeper and I am sorry that you have had so much trouble with all of this. My response may come too late but perhaps someone else will search and this will help.

I will try to keep this as short as possible.  This is related to those who have toggled on the Deposit feature in the Account and Settings and want to use it to reduce an invoice by an amount already received in advance.  Between this and the other post, someone was saying that they were receiving an error to select an account to deposit to but couldn't see it.  The "deposit to" is shown in the center of the Invoice screen once you enter an amount into the deposit box and tab out of the box.  If you don't enter an amount and tab out, or remove the amount from the box the deposit to (which also includes a payment method and reference number) will disappear.

Ok, so that is how to enter it.  Now comes the bigger issue.  When you receive money in advance from your client you post it to a liability because you owe your service or product to them at some point in the future.  It is not income until you have earned it.  Then when you reduce the invoice (which is your earned income) by putting the amount you previously received in the box you need that amount to offset the liability (or to the account the original money was posted to; even though anything other than a liability is not the right way to do it from an accounting perspective).  The problem is that QB only allows you to use Asset account to deposit to not another account (again it should be liability).  This is an error on QB part.  So the workaround for now:

1. Create a liability account called Customer Deposits (or whatever name works for you). 
2. Create another asset account called something similar... I might use Customer Deposit Temp.
3. When you receive the original amount deposit it to the Customer Deposits liability (if you invoice for this make sure your item maps it to the liability account).
4. When you use the deposit, in the deposit box, deposit it to the temp asset account.
5. Then create a Journal Entry.  Your first line will be the Liability account and the amount will go to the Debit side (debits first).  The second line will be the temp account and the amount will go to the Credit side.  This journal entry will move the money from the asset account and offset your liability.  Eash persons books are slightly different so the deposit received may be more than you are using on a particular invoice.  Always journal the amount you used in the invoice so that you 0 out the temp account right away.

Please feel free to reach out to me if I can help.