To add services to a site's content library, you must register them to ArcGIS Online. When working with map and feature services, you can register services containing multiple layers, or register the individual layers themselves.
To learn more about registering services and service configuration, see Server configuration details.
Individual layers
Individual layers provide greater control over the item's metadata—you can edit individual titles and descriptions in ArcGIS Online. Each layer will have different tags as set in ArcGIS Online, which will provide better search results for the end user.
Services with multiple layers
This is a quicker way of getting your data live, but it gives you less control over search results and an item's metadata. All layers in the service will have the same description and the same tags, and all layers will appear in search results when a tag or the service name is called.