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Speaking for Management Suite, it can only handle SQL Authentication.
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That document is specific for Management Suite. For Service Desk you can use either SQL or Integrated security. Within Configuration Centre where you specify the database connection details there is a checkbox to determine how to connect. I can say that a very high percentage of customers use SQL authentication rather than integrated.
If you do decide to use integrated security you need to configure which user to connect as. Each application sits in an application pool of your choosing and it will use the identity of that application pool to connect to SQL Server. You can configure the application pool identity within Configuration Centre.