Hi,
Cisco Media Group can includes all the ports that you have licensed in your IVR. You can have several Media Groups depends on the functionality that you would like to associated to those ports: a media group ports for ports, for example, with TTS support, another one with ASR support, and so on.
You could use CTI Port Groups to associate a number of ports to differente applications: for example, one CTI Port Group for queue applications, another one for self-service application 1, and so on.
There could be other methodologies to implement this groups.
Hope this helps,
Juan Luis