Are you talking specifically about having services that you've published to your own ArcGIS Server show up in search for layers? You have to add them to My Content.
My Content>Add Item> Item is on the web then specify the URL to your web service. In the map viewer, when you search for layers, you may need to uncheck the box that says search "within map area".
Also, if this service is behind a firewall, some operations in arcgis online require it to be externally accessible. But, as long as the browser is running inside your firewall, you'll be able to display it, but some other operations may not work, like printing.
Thanks,
Mike