AMT Director has it's own AMT provisioning server built into it. When using the development tools, the prefered way is to use AMT Director to handle the provisioning for AMT Commander. However, AMT Commander will work on systems provisioned by Intel SCS. Using the latest release of AMT Development Tool Kit (0.44) installed on the same machine as the Intel SCS, you should be able to connect to your AMT systems using AMT Commander without any changes from default settings. You'll need to make sure that the user name and password you are using to connect to the AMT system is the same as is set in the ACL settings in the Intel SCS profile (ex. if you used a Kerberos user name and password, you'll need to use the Kerberos log in credentials in AMT Commander).
If you are using TLS and don't have AMT Commander installed on the same machine as the SCS, you'll need to import the TLS Authentication certificate into AMT Commander. The tool to do this is located in AMT Commander, under the File menu in Certificate Manager.
Hope this helps!