First make sure that you have the Security configured and working, on your IIS
Then Configure you ArcGIS Server as follows
1) Users and roles from an existing enterprise system (LDAP or Windows Domain)
or
2) Users from an existing enterprise system (LDAP or Windows Domain) and roles from ArcGIS Server's built-in store
You can create Roles on your ArcGIS server and add users there. The give a 16 digit key that you will use to configure web adaptor. Once you configure web adaptor everything should be set.
The Security settings on your ArcGIS Security page should look something like this if you are using Windows Authentication
Configuration Settings | |
---|
User Store: | Windows Domain |
Role Store: | ArcGIS Server Built-in |
Authentication Tier | Web |
Authentication Mode: | Web |