You are adding in the email in the correct location for this part of the setup. It should recognize the value you have in the wa_settings folder and use that. I was able to confirm this in the code for the email receipt itself. The same should go for any other cc or bcc that you setup in the admin back end. The code is configured to take a look at the settings to get the cc and bcc values.
Since you are able to send the emails ok there might be a problem with the cc and bcc part. I have opened a ticket for you on this issue so that it can be looked into further. To update your ticket login and visit your support history.