VJ,
I haven't used the Siemens software myself, so can't comment on its differences with respect to JaamSim.
Regarding Setup (and Setdown), you need to include this time in the ServiceTime input for a Server or EntityProcessor. This input accepts an expression, so it is just a matter of writing a suitable expression with one term for setup time and another for processing time.
Model each worker as a ResourceUnit and collect them in one or more ResourcePools. Working time can be modelled using the TimeSeries and TimeSeriesThreshold objects and entering this threshold to the OperatingThreshold input for each of the ResourceUnits. One of the examples in 'Getting Started' chapter of the user manual shows how to model shifts with the TimeSeries and TimeSeriesThreshold objects. See section 3.3.3.
Harry