For a configured search layer you'll need to add a line that sets the placeholder in main.js around line 902. If you only have one search layer configured just add something like this:
source.placeholder = "My Custom Placeholder Text";
If you have more than one search layer you'll want to check the layer title or id first to ensure you get the correct placeholder text for the layer you are looking for. For the next release of ArcGIS Online we plan to provide an easier way for you to setup and configure the placeholders for search layers.
Another alternative would be to update the config.js file and add a new property called placeholder to the searchLayers section. Then you could check in main.js to see if you have a placeholder defined and then use that value. So you'd update config.js like this;
"searchLayers":[{
"id": "myLayerId",
"fields": ["parcelid"],
"placeholder": "My Custom Placeholder"
}],
Then update main.js as follows:
source.searchFields = layer.fields;
source.displayField = layer.fields[0];
if(layer.placeholder){
source.placeholder = layer.placeholder;
}