Selecting output channels for analysis in Electroacoustics Toolbox only allows you to see signals that are generated within the program, itself. In order to view signals from other applications, you may want to take a look at the tutorials regarding
Soundflower and
Jack. The tutorials refer to SignalScope, but the approach is essentially the same for Electroacoustics Toolbox (or any audio program). (Jack also provides Audio Unit and VST plug-ins for more signal routing possibilities from your DAW.)
Ben