Unfortunately, the popups are not accessible from this application. You can only get additional information for map service layers (not layers based on shapefiles and csvs). And the information returned is formatted using the classic ArcGIS Desktop Identify tool.
This application was written before popups and support for shapefiles and CSVs were available. We plan to update it in the near future. If you want the popups now, and are comfortable with a little programming, take a look at the side-by-side viewer, which does support popups.
Thanks,
Mike
