Applies to Google Apps customers only.
You can control who can see Appogee HR in the App Launcher.
Just turn the app on or off for those people in your Admin console. People who have the app turned on will see it in their app launcher and be able to login using the Google Apps login method.
For instructions on how to turn on/off Appogee HR for specific Google Apps organisational units please see this Google Apps Administrator help article: https://support.google.com/a/answer/172931