When your client has the Vat Calculation Service (VCS) switched on in Amazon Seller Central, A2X will receive a great level of detail on the VAT transactions that are passing through the seller account. Usually 20% VAT Rate products and Zero-Rated products will be clearly differentiated in A2X already. This allows you to allocate separate tax codes to each.
In Shopify we also generally see a tidy split between Zero-Rated and Standard Rated products for tax coding. We can also enable further VAT functionality in Shopify, where required.
Sometimes we see that a seller has a special product that attracts a special rate of VAT. Good examples in the UK are baby car seats, firewood and certain types of hygiene products, which all have a 5% tax rate. In this case, we would set up a separate product type grouping in A2X for these items. This then isolates them for special tax treatment and you can apply your 5% VAT Rate from Xero or QBO.
If you have any questions reach out to the support team for more information.