Sorry about the delay, but best practice would be to use the included task sequence. There are two main ways of doing a system discovery using ACUConfig. The default way (the way the task sequence runs system discovery) stores the data locally in the registry. The other way is to have ACUConfig report back to the SCS server (this requires the computer to already be configured, and have a record in the SCS database) and update the clients information.
Using the discovery task sequence will allow SCCM to discover Intel AMT systems and add them to the correct collections.