We have products which would fall in different GST categories for e.g. 12% and 18% . Kindly guide us how to set up the same.
Go to Settings → Taxes in your Shopify admin and click on India.
Enter the 9% CGST tax rate into the Country Tax field.
For the state your store is based in, add the SGST (or UTGST) rate and choose to add to 9% federal tax from the drop-down.
Much easier to use an invoicing application like https://apps.shopify.com/shipturtle
It is developed considering the challenges of GST