This blog is to help Portal Administrators determine between the options for creating users in 10.3 when configured for Enterprise Accounts - Windows Active Directory. I experimented with the options for creating users in Portal for ArcGIS. In 10.3 we currently have three options to add members using enterprise accounts. You can do automatic registration which automatically registers any user when the visit the portal webpage. The second method is to individually create users through the Portal Admin Directory (https://computername/portal/portaladmin/security/users/createUser). The third and final method is through a bulk command line utility (CreateUsers.bat). At 10.3 I recommend the third option of using the command line utility, it creates the users with the same properties as the automatic registration (2nd option). Unfortunately the Add Members tool on the My Organizations tab only allows you to add members using the Built In store (not enterprise log ins).
A little bit about the differences between the 2nd and 3rd options. The second method creates the users via the windows active directory but they still must log in to the portal for the first time to become recognized, this was a hassle because the Portal Log in page is hard to find. It’s not the default homepage and could only be accessed through visiting the Map page. Also, this method activates the sign out property for each user (may be helpful if you want this). Finally the members Username and Name (as seen on the My Organization tab) is inconsistent with our automatic registration properties. The Names are Last Name, First and Username includes the @DOMAIN, when individually created the Names are First Name Last (no comma) and the Username does not include the domain. Again, the 3rd option which uses the bulk command line utility creates a user which appears identical in properties to the automatic registration. I've attached outlined instructions for this method though you can also review Esri's Help for Adding Members to Portal.
Last but not least, I understand that in 10.3.1 this changes so you can disregard my blog or hopefully I have revisited this for updates.
Hope this helps and good luck!