When a user logs on, he can use his Active Directory account. Help Desk Server will query your AD to authenticate the user. It will then automatically add or update the corresponding user account in Help Desk Server.
Note that the authentication is done by Active Directory. The authorization (ie. what can the user do within Help Desk Server) is done in Help Desk Server. By default, all users are treated as type "Other Employees" in the help desk. To set up some users as Help Desk Technician or Help Desk Manager, you need to go to the web interface and modify their user accounts.