I am not sure if I understand your question correctly but AMT exposes two interfaces to communicate depending on the version of the firmware. You can communicate with AMT using SOAP API's or WS-Man (starting with AMT 3.0)API's. Please let us know if you have further questions.
The SDK and the DTK both have some command line tools you could use to script simple tasks like waking up a computer, etc. The Intel AMT Terminal in the DTK also has a built-in scripting system so you can automate, for example, going into the BIOS of a computer remotly and changing settings.
Generally, you would run there management commands on a different computer, not on the computer you want to manage.
Ylian (Intel AMT Blog)