EnergyPlus tries to emulate real world systems in a way consistent with the time step granularity most often used in annual simulations. Equipment controls are setup using objects that allow the user to emulate "normal" control strategies. For example, an economizer has several control options to either use enthalpy limits, drybulb, or, or, or. Another example are the plant sequencing objects to control for example multiple chillers. Finally, EMS can deliver building management level or extra special control where required (and much much more).

If you set a space to be for example cooled to a setpoint, all equipment will strive to reach that setpoint within the limits of each of the equipments. However, you could write an EMS to slide the set points dynamically to optimize the systems. Some equipments may have this kind of control captured in other ways such as lag times, or performance curves.

If your goals are very equipment performance heavy, you may have to consider alternative programs like TrnSys and program your own modules for controls and components. Controls in TrnSys must be largely setup by the user. Far more difficult but more flexible and often transparent (at least to the person setting it up). The downside is that many "assemblies" need to be setup from scratch, so the first time user invests a lot of time just building subassemblies and assemblies for equipment plants and their controls. To make subassemblies and assemblies more reusable, considerable time is invested making control components like PID controllers scale with equipment capacities. Two other down sides are that there are no autosizing options and most reporting must be user defined.