I am not sure what you are referring to about MSConfig. I assume you are talking about the Services tab, but I don't see any 'auto restore' feature.
By Processes, I assume you are talking about the list that is shown in the Task Manager on the Processes tab. The processes listed there are either processes used by running Applications or installed Services.
To get rid of processes used by running Applications, quit the Application running them. An example of this is the process, notepad.exe. Notepad.exe is shown because the Notepad is open. Close Notepad and the process, notepad.exe, will be removed from the processes list. Another example is iexplore.exe, which is connected to Internet Explorer. If any of these are appearing on the list without you running any applications, they can be removed by finding out what is starting them at startup and removing it from startup (msconfig and Speed Startup can help you with this).
The installed Services shown in Processes are not actually running, even though msconfig reports them as running. Instead they are listed in the registry as installed. So there really is no problem with having these on the Processes list because they really are not running and are not using any resources. If you remove these (they can be removed by uninstalling the service) there may be problems when the associated application is run. Not all of the Services shown in MSConfig are shown in the Processes list.