See Server configuration details for best practices on how you can prepare services to share through ArcGIS Enterprise Sites.
Individual layers provide greater control over an item's metadata and you can edit individual titles and descriptions in Enterprise. Each layer includes tags as set in Enterprise which improve the search experience for people visiting your site.
Services containing multiple layers
Registering services containing multiple layers is a quicker way of making data live, but you have less control over the search results and an item's metadata. All layers in the service have the same description and the same tags and all layers appear in search results when a tag or the service name is used.