Correct way to stop SQL Server (through automation)
You are safe either which way you go. SERVICES.MSC and POWERSHELL command lines are EQUAL functions to MSSQL Configuration manager...

Configuration manager is also used to control instances, etc etc but the function of starting and stopping a service is the same no matter which method you choose.

Some people have their own ways of doing things, for example to quit an application, you can do File > Exit. Or you can do ALT+F4, they are both the same function...

Please view this link below for additional information and helpful details. This covers all of the different methods (SQL configuration mgr, SSMS, Commandline etc)

https://msdn.microsoft.com/en-us/library/hh403394.aspx

UPDATE regarding Failover Cluster Instance...

If the instance is clustered, use of any of the above suggestions does not apply and should not be used. For a FCI you need to utilize Cluster Manager or the FailoverClusters PowerShell module commands.