How to apply refund to customer invoice

Our customers need to make a deposit of $200 before we can submit works.

We create an invoice and then apply the $200 payment to the invoice. If the works come to the total of being under $200 the difference is refunded.

For the works a new invoice is completed and then the deposit is deducted of the amount.

The issue Im having is that when I'm recording the deposit reckon is including the gst amount from the deposit and adding it to the balance that's due, but not giving the correct due amount.

If i tick the amount to include tax box then the balance goes into negative and i cant record the invoice without an adjustment. But when i create the adjustment its not applying to the invoice when i allocated it refund….