It is easiest to use the HVACTemplates to create the initial chilled water and condenser water plants.
Once you've added all of the HVACTemplates for the multiple chillers towers and plantloops, simulate.
EnergyPlus will expand the HVACTemplates into their component objects and write a file with the name FILENAME.expidf
Rename this file as FILENAME_Expanded.idf and you can then modify the expanded template file with the .idf editor or a text editor, whichever you prefer.
Now replace your Pump:VariableSpeed objects with HeaderedPumps:VariableSpeed and Pump:ConstantSpeed with HeaderedPumps:ConstantSpeed
the Headered Pump objects have fields that allow you to input the total flowrate, the number of pumps in the bank, and the flow sequencing control in addition to the typical pump inputs.
Maintain the same node names that were in the initial pumps and everything should hook up nicely. be sure to search the file for any instances of the phrase "Pump:" and replace with "HeaderedPumps:"... its easy to forget to change the pump reference in the Branch object for the pumps