Amber,
Sure the code that need to be changed is in the jimu.js/LayerInfos.js _getLayerTitle function:
notice lines 8 -27 are commented out to prevent the adding of the service name to the layer title.
_getLayerTitle: function(layer) {
if(layer.title) {
return layer.title;
}
var title = layer.label || layer.name || "";
return title || layer.id;
},