If you check the Engineering Reference document for how EnergyPlus calculates heat transfer through the external surface and internal surface of each construction assembly, you'll find that calculations are done on a heat transfer per area basis. EnergyPlus then uses the area information from the building and fenestration surface objects in the model to calculate a total heat transfer. This means that if you were to remove a surface between two adjacent zones, then EnergyPlus is unable to calculate heat transfer between them! The same can be said for solar radiation (daylighting), but in this case if there is no transparent surface (window, eg.) between two adjacent zones, EnergyPlus is unable to calculate daylight transfer between them. Even if there is a void in between zones in reality, EnergyPlus still requires some sort of surface to properly calculate energy transfer (thermal, solar, etc.).
The best way to capture both thermal and daylight effects is to model a "high transfer window" that has high transmittance to allow more solar distribution and high U-value to allow more thermal heat transfer. As far as placing these "high transfer windows", at the very least you should use your horizontal zoning to allow daylight to pass from the upper zone into the three lower zones. If you think that having one large upper zone at a single temperature is too simplistic, then use vertical zoning in combination (three upper zones and three lower zones).
NOTE: Depending upon how much detail you want to capture, you can also include air mixing effects between zones through the Zone Mixing and/or Zone Cross Mixing objects. These include some convection heat transfer between adjacent zones instead of only modeling conduction heat transfer based on temperature difference between adjacent zones.
@Gurneet, please use existing tags (including which software you are using) rather than creating custom tags that people are unlikely to be subscribed to or to search for.