Not sure I understand 100% what you're getting at, but if you want airflow between zones then a surface in both zones, that represent the airflow component between the zones, has to have a materiel applied that is designated as a zone boundary and as an air-flow surface in the EnVi Construction node for the material. Make the material solid wall construction (you can have a air cavities between solid layers) for one zone and make the opposite construction for the other zone. When you export the EnVi geometry and go to the EnVi Network node tree you should see two the two zone nodes each with a brown boundary socket and a red airflow socket (red if the construction is a wall - would be green for a window or door). You will get one socket for each face that the airflow material is applied to.
Connect the two zone boundary sockets together and connect the two red airflow sockets via a surface flow node. In the surface flow node you can then set the nature of the flow component. Bear in mind that EnergyPlus requires that at least two flow components or surfaces are specified within each zone when creating an airflow network.
Ryan