Hi Abdul,
"Maintain Prefix Number" is only required in DEV client where you are creating the WF templates.
"Check HR Control tables" : In some customer sites, I have seen this settings is not activated and people are bit apprehensive switching in ON thinking it might cause issues with HR. Usually when you do a auto customising, you end up few error messages which can be fixed by running standard reports. This setting should be activated and there are no HR implications in doing so. Refer SAP note 60801. Refer to thread mentioned by Murali Krishna..
Hope it helps
Regards
Sandy