You can add your filter in the web map prior to creating the web map application. Next to the layer you want to add the filter to, click the arrow/carrot to the right and choose the filter option. Also see:
http://blogs.esri.com/esri/arcgis/2013/04/22/filtering-performing-analysis-and-building-a-web-map-ap...cation-with-arcgis-online/
Hope this helps....