Hi Manoj,
usually, you start with a working setup that is capable to be run from the command line. This is entirely FM-specific and outside of CAESES.
In the current version of CAESES we provide a tutorial on the geometry preparation for FM, based on the Maritime Workflow introduced in CAESES 5.3. Assuming you've got the latest version of CAESES installed, you can find it here: http://localhost:65038/tutorials/maritime/software-connection/fine-marine-pre-processing . This geometry should be exported either as parasolid or as multibody stl.
At this point the above-mentioned workflow comes in. Please identify all relevant input files and provide them from the software connector. Define case-specific values by parameters. Put the command you used to run the setup from the command line into "ExecutionSettings|Arguments" (possibly preceded by "bin/bash"). Run the case for one geometry from the software connector and define all relevant result files within the software connector for further post-processing.
Hope this helps!
Cheers,
Hannes