Can you please specify a bit more detail? A screen capture, for example, would be very helpful.

You don't have to specify it, but source and result data are set as user parameters by default when you create a new workspace and the FMEServerJobSubmitter allows you to set those user parameters. If you don't set them it'll use whatever you have specified as default in the workspace.

Usually source and result data are different on FME Server compared to the FME Desktop where you develop it, and an FMEServerJobSubmitter is often used to control complex workflows so in many cases you do want to set those parameters.

You can also remove the parameters alltogether in the child workspace but that removes any control you have over those dataset locations.