Create file with one FCU using the HVAC Templates, and run this file.
This will create an 'expanded idf' with file suffix .expidf
Rename this file as suffix .idf so you can edit and run this file directly
Using the template will show you which objects are necessary to model the FCU. Duplicate them individually and append some differentiator in the name of objects, for example, if you used f1:Zone1 FCU1 change the second one to f1:Zone1 FCU2
You will need to create a node list for the supply and exhust connections in the ZoneHVAC:EquipmentConnections object to allow for multiple zone air inlet nodes and return or exhaust nodes
In zonehvac:equipmentlist, you will have two fan coil units, set the priority of the ventilation only FCU to 1 so that it operated first. You will also need to hard size this fan coil unit.
In the recirculating FCU set the OA flow to zero.
While I haven't specifically tried to model this system, I think this should work okay.