Under the [GroupWiseSetup] section in the SETUP.CFG file, the parameter StopService can be added. According to the documentation, this parameter will stop a service before the install starts and restarts it after the install has finished. It is very unclear exactly what information is needed for this section
The exact name of the service itself rather than the name of the executable. For example if VMWare Tools is the service that is to stop, using the real name of the service, VMware Tools Service, or the process name, VMwareService.exe, will both fail.
To find the Service name, open Control Panel -> Administrative Tools -> Services and scroll through the list until the desired service is found. Once the desired service is located, highlight this service. Right click and select Properties. Under the General tab the first line is the Service name. This is the name that will need to be used on the StopServices line in the SETUP.CFG.
In the above example, the correct service name for stopping VMWare Tools is VMTools