It's possible to deduct tax, and shipping tax, from the order total of all WooCommerce orders when they are processed by Shiptheory.
To achieve this, go to the Advanced Settings section of the WooCommerce settings page. To deduct tax from the order total, from the Apply Tax Deduction option select Yes, deduct tax. This will also result in tax being deducted from products that are part of the order.
To deduct any shipping tax, from the same page, from the Apply Shipping Tax Deduction select Yes, deduct shipping tax.
Select the Save button to save your changes.
If you have any queries about this integration our support team would be happy to help you out.