When you install and configure ArcGIS Server, there are two main accounts that you will work with: the ArcGIS Server account and the primary site administrator account. These are different accounts, and it's important that you understand their distinct functions.
The ArcGIS Server account
The ArcGIS Server account is a new or existing operating system account that runs the ArcGIS Server Windows service. You specify the ArcGIS Server account at the time you complete the ArcGIS Server installation wizard.
You need to give the ArcGIS Server account permissions to access your GIS data, in the same way that you gave the SOC account permissions to your data in previous versions of ArcGIS Server.
To learn more about the ArcGIS Server account, see The ArcGIS Server account.
The primary site administrator account
After you install your software, you create the ArcGIS Server site. At this time you need to provide the name and password for a new account that you will initially use to log in to Manager and administer ArcGIS Server. This account is called the primary site administrator.
The primary site administrator is not an operating system account, and it has no relation to the ArcGIS Server account. The primary site administrator name and password are used only with ArcGIS Server, and they are stored by ArcGIS Server. Later, you can create other administrative accounts and disable the primary site administrator if you choose.
To learn more about specifying the primary site administrator account, see Creating a new site.