Enabling single sign-on for App Controller
By default when you load the App Controller page, you are prompted to enter a username in the format domain\username and enter your password.
However you can enable App Controller to use your logged on credentials to automatically sign in. This is actually documented in the Online Help 
.
You just need to enable integrated authentication on the /api node of the App Controller website in IIS.
Directly from the help pages:
How to Enable Single Sign-On for App Controller
By default, App Controller is enabled to prompt users to sign in by entering their Active Directory user name and password. The following procedure describes how to configure App Controller to use the user’s current Windows credentials to automatically sign on.
To enable single sign-on
Open IIS manager on the App Controller server.
Select the App Controller website.
Expand the website and select the /api node.
Click Authentication.
Enable Windows Integrated Authentication.
Disable Basic Authentication.