Make sure that the source and destination parameters are published parameters. Then use the published parameter names as flags in the batch file. It'll look something like this:

fme myworkspace.fmw --SourceDataset_ESRISHAPE "c:\\data\\parks.shp" --DestDataset_ESRISHAPE "C:\\SHP\\output.shp"

You can find an example of the command line entry to use at the top of the log file when you run the workspace in Workbench.

Thanks @ryanatsafe. I was actually using the command line from the log. with below syntax on my bat file

C:\\apps\\FME\\fme.exe E:\\500-GIS\\01-ESRI\\AverageDepth.fmw

--SourceDataset_FILEGDB "E:\\500-GIS\\01-ESRI\\Created_Shapefiles\\Sewer2018.gdb"

--DestDataset_FILEGDB "E:\\500-GIS\\01-ESRI\\Created_Shapefiles\\Sewer2018.gdb"

However when I change my source&dest file path the output still writes on my original file path (path provided inside my fme)

Make sure the --SourceDataset_FILEGDB and --DestDataset_FILEGDB are on the same line as the C:\\apps\\FME\\fme.exe E:\\500-GIS\\01-ESRI\\AverageDepth.fmw. The log file has line-breaks to clean up the formatting, but in the actual command it all has to be on the same line. Because the flags are optional, if they are on a separate line then the FMW file will use the default values.

Another issue to be aware of is that FME can only create so many folders when it is running a translation. It should be able to handle what you have set, but double check to see if the folder Created_Shapefiles already exists. If not, create it manually.