Yes it is possible to model multiple thermal zones using only one HVAC system.
The ZoneControl:Thermostat object is used to report the load in a specific zone. If more than one zone is served by the HVAC system, a master zone is used to report the load of that zone to the HVAC system. Slave zone(s) will get what they get based on the air flow balance of the air distribution system. The master zone is selected based on a load analysis that shows how the other zone temperatures vary as a function of master zone temperature/load. Testing and balancing of multiple zone air distribution systems will set the air flow rate to each zone to balance the system flow rate so that when the master zone load is satisfied, the slave zone will also be satisfied within a reasonable margin. If the load profiles of all zone are not identical, then it is likely that slave zones will not exactly meet the master zone temperature set point.
The ZoneHVAC:EquipmentList specifies all equipment defined for use in a single thermal zone. This can be a ZoneHVAC equipment, zone exhaust fans used with ZoneHVAC equipment, ZoneHVAC used with AirloopHVAC equipment, etc. There are many combinations and configurations that can be entered in the zone equipment list. It's is a good idea to look at many example files to get an idea of different configuration options. The example files are meant to guide users in the connection requirements for each object type. See the ExampleFiles-ObjectsLink.html doc to see which example file exemplifies a specific object.
The fan coil, more specifically the ZoneHVAC:FourPipeFanCoil, is meant to serve a single thermal zone. For this reason, only one fan coil should be specified in any zone equipment list (because the inlet and outlet of the fan coil must connect to zone inlet and exhaust nodes). If more than one zone is served by a single HVAC system, then the AirloopHVAC system should be used. The AirloopHVAC objects serve multiple zones, can use a master zone thermostat, and requires zone air balancing to maintain acceptable zone conditions.
As a final thought, the fan coil unit, using water coils, can also be modeled using the AirloopHVAC:UnitarySystem object and the results should be the same. The difference is that the fan coil model only serves a single zone while the AirloopHVAC can serve multiple zone. Another slight difference is how zone equipment models outdoor air versus the use of an outdoor air controller for air loops. If each of these serve a single zone, the answer should be the same as long as the outdoor air quantities are 0 or made to be the same.
You may be confusing a space vs. a zone. You can have multiple spaces in one thermal zone in EnergyPlus, with one thermostat control. If they are indeed two different zones - meaning they have two separate thermostats, how do you plan on controlling the HVAC equipment in reality with one device?
Yes, They are two separate thermal zones using one fan coil. I am trying to model the fan coil assuming it is controlled by the thermostat where the fan coil is located. I think it is closer to reality. Thanks.