Hi Cat -- In Sonnet, there is only one kind of port. It is an infinitesimal gap with a voltage impressed across it. This port can be put in different locations. For example, on the edge (so that the sidewall provides a perfect ground reference), it is called a sidewall port. On the interior, it is called an interior port. However, it now no longer has the same ground reference as the sidewall ports. So, you can click an option (by double clicking on the port) to make it an auto-grounded port. In this case vias are added to ground to make the ground refernce. If the port is a via, then we call it a via port. For RFID, just build on the circuits I attached above, and you should do just fine.
As for HFSS, I just know the high level trade-offs. I think it is likely that port choice will be important, but I can not advise you on which port to use. If you are on support, by all means talk to their support on this matter.
As for CST, if you are on support or considering purchase and in North America, we (at Sonnet) will be glad to help. I do not have the knowledge to help you on CST, however, we do have several support employees who are extremely knowledgeable on the matter. Otherwise contact CST directly.
And of course, I am sure there are others who can provide the needed information right here on this forum.