Once the Energy Model is created, the masses will be merged by and you will see a warning message from Revit. We recommend modelling floor by floor (storey by storey) as it gives more control over the surfaces in the application.
Zones may be created, and finer control is possible for each storey (eg. separate glazing specifications, glazed areas, fritting etc). Masses modeled as one volume in Revit will be assigned one Surface over the entire orientation and individual control for each storey will not be possible.