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Here is a KB on how to set up a certificate on a web service connection:
https://www.qvera.com/kb//index.php/909/how-do-i-associate-certificates-with-my-qie-connections
Once you set up the web service connection to the https endpoint you are connecting to you can then select web service on the destination and select the web service connection you setup.
Basically, the HTTPS is set up on the web service connection and you point the destination to that connection.