When using Unstack with Shopify almost all of your store is managed through Unstack. However, there are a couple parts that are not managed through Unstack; specifically the checkout process and the order confirmation page in particular.
These are completely handled by Shopify, and changes to them need to be made through Shopify.
Adding custom scripts to your order confirmation page
As these pages are being handled by Shopify, scripts and tracking codes will need to be added via Shopify, not Unstack.