As instructed handling upfront retainers. I created an other current liability account for the retainers. I created an item, for the retainer as "other charge" linked that to my liability account. 

When I receive a retainer from a customer, I create a sales receipt for the deposit amount. Those funds are deposited in my main operating account. When the job is complete, I create an invoice for the total repair amount. Then create a credit memo for the amount of the initial deposit, using the same line item and apply it to the invoice. 

Now all of a sudden when I pay sales tax, my non-taxable sales are now in the negative. Which is absurd.