File geodatabases provide a convenient method for data storage that can be used with both ArcGIS for Server Workgroup and Enterprise licenses. The file geodatabases should be placed or created on an Elastic Block Store (EBS) of your ArcGIS Server on Amazon Web Services instances so they can be moved between instances more easily.
To help you decide whether you want to use a file geodatabase to store your data for use with ArcGIS for Server, see Data storage considerations for an ArcGIS Server site.