Tax settings within Marketplace Connect is now very simple:
If the marketplace sends the tax we will send this with your Shopify order.
If the marketplace is responsible for collecting and remitting the taxes to the relevant tax authority we will set the order as channel liable.
If you are on the legacy tax settings, the screenshot below will be visible in your settings page (here for Amazon). You will only need to select this button once and it will not show again.
For further assistance, please reach out to marketplace-connect@shopify.com