There is currently no documentation on the built-in store GEP uses to manage its users. Similar to ArcGIS for Server, you can use the Manager to created users and assign them either 'User' 'Publisher' or 'Administrator' roles. Only 'Administrators' can log in to GEP Manager and administer the Inputs, Outputs, Services, and other configurable items. You must be a 'Publisher' or 'Administrator' to run the Service Designer web application.
The GEP approach to its "User Roles" and "Identity Store" is changing with the 10.2.1 release due out Winter 2013. This next product release will better support server connections to ArcGIS Online and server connections to Portal for ArcGIS. We're also working on supporting the federated security model used by Portal and AGOL for enterprise authentication.
Chris - I wanted to clarify what we are planning on releasing at the Winter 2013 ArcGIS release. At the Winter 2013 release we will have improved support for server connections to ArcGIS Online as well as server connections to Portal for ArcGIS.
At the Spring 2014 release we are planning to support the federated security model used by Portal and AGOL for enterprise authentication and at that time we will switch to utilizing the ArcGIS Server/Portal "User Roles" and "Identity Store".
Hope this helps to clarify and set expectations for timing of these capabilities, Adam Mollenkopf ArcGIS GeoEvent Processor for Server - Product Lead