Answering for the benefit of others with a similar query.
Instead of generating shipping labels externally and importing the tracking numbers in bulk using CSV, you can check out the Shopify Multi Carrier Shipping Label app, which will help you to integrate directly with carrier account to generate the shipping label and send the live tracking to customers.
I know this is a little late but I wanted to leave an answer just in case someone comes across this in the future.
If you're looking for a simple way to update your tracking numbers by the order ID our app, EZ Fulfill, can help. We allow you to bulk update your tracking numbers and mark orders fulfilled via manual upload, SFTP, FTP or Dropbox. If you have any further questions feel free to reach out and let us know.