This post is years old and not one single person has been able to answer the question.  Here we are and the problem still exists.  This is one of the most frustrating things about Quickbooks Customer Service is they don't actually know what they are doing nor do they really read posters questions...ever.

I have the same problem as the original poster. ... When using the deposit "box", that is when you have turned the "deposit" box toggle on and input a number into it, the question was where does the deposit go? If an employee reads this... we are not talking about payments, we are not talking about undeposited funds, or a custom field on the invoice/sales receipt.  We are talking about QB feature that can be turned on and off that allows an invoice/sales receipt to be reduced without an actual payment being made and without an associated service/line item.

To further clarify, in my situation, I see where the amount put in the "deposit box" is going.  It is somehow increasing the Bank Accounts heading... a non-existent account.  So, a clarifying question might be how do you change the account the money placed in the deposit box goes to? It does not go to undeposited funds.  If it does, then in my case, and I'm guessing the original poster's question it has been changed so how did that happen?