Configuring the Cloud Softphone app.
Most settings (domain, codec order, and many more) you can change in the provisioning options in your app in the cloud softphone web portal. You would create an editable copy of your app, make the change in provisioning options of the editable copy, then submit an editable copy for review. Once it is approved, you can make the change live.
If you are using external provisioning, you can also set most account-level settings in account xml.