We do not add a deduction for partial invoices on the final invoice as partial invoices can be used in different ways.
If you want to show that a customer has paid part of the full amount then you can add a negative line item for the value they have already paid.
You can raise a partial invoice, then alter this later and turn it into a final invoice when you're ready to close the job down (read here how to change an invoice to a final one). When the customer pays in different instalments, you can add the separate payments to reflect this on one invoice.