Ok, I have a work around for those who want to use the deposit box on the invoice. I will post that response on the other thread https://quickbooks.intuit.com/learn-support/en-us/reports-and-accounting/re-how-do-i-map-the-deposit....

@soloithz23 While the tax might be calculating correctly (and I have never used DAVO) you need to check on something.  The deposit box is intended to reduce the balance of the invoice using a payment previously received from your client.  So A., if you put 500 in that box, you are saying you previously received that $500.  Where did you deposit that original $500?  When you then enter $500 in the box, it requires you to deposit the $500 to some account.  Where are you depositing that?  

The correct accounting way is that the original $500 should be categorized to a liability account.  And the $500 in the box needs to be put in that same account.  However, QB doesn't allow this.  So my guess is that you are going to have $500 in two different accounts that never 0 out and thus your books are incorrect.