I created my own printing layout MXD's and created a custom print service per this method. I then configured the Web AppBuilder to use the custom print service. Everything seems to work great except the legend. I have configured several map layers in the controlling ArcGIS.com map to NOT display in the legend of the Web App when they are checked on. The custom print service does not seem to honor this. It simply shows every layer that is checked on in the WebApp at the time of printing, even though the controlling ArcGIS.com map is set to not display certain layers.
Does anyone know if there is a legend setting in the MXD used to make a custom print service that would prevent all these unwanted layers that are checked on from showing in the legend? http://resources.arcgis.com/en/help/main/10.2/index.html#/Tutorial_Publishing_additional_services_for_printing/0154000005n1000000/