How to Configure FortiClient Compliance with both EMS and FortiGate?

I'd like to know how to configure FortiClient compliance but cannot find any documentation on how to do this for environments that have both a FortiGate as well as an EMS server.  Is there any documentation on this setup?  I just tried poking around myself but didn't have any luck.  In my FortiGate I created a FortiClient Compliance Profile, then logged into EMS and imported that profile but it just imported as a regular EMS profile with default firewall, sandbox, etc. settings.  Any help or point in the right direction is appreciated.  Thanks!