I was looking into the new wowza 4 and spun up a ec2 to take a look. Seems that for the instance publish user/pass is added in sequence to the main conf/publish.password instead of creating a separate conf/[instance]/publish.password. Is this correct?
The Administrative username and password definition is requested while running the installer. This will initially populate the [install-dir]/conf/admin.password file. This will not effect the Publish.password file, where incoming credentials are stored.
The "Publishers" are added manually, as required, when configuring Wowza Streaming Engine Manager. By default, a live streaming application is set to require RTMP and RTSP authentication. If an application does not accept an incoming stream, one of the first items to check are the "Publishers" in the Server configuration section of Wowza Streaming Engine Manager.