how to stop background app refreshing in iOS9 I'm using the latest version of iOS on iphone 5s  (till the date of this post) and I want to stop apps like whatsapp and so from refreshing in the background but without stopping notifications of these apps so that I can get notifications ONLY when running these apps.
When I go to the app settings in SETTINGS and disable ( Background App Refresh ) I still get notifications when someone msg me . 
Does that means the apps still working in the background ?
There is a difference between background app refresh and push notifications. Push notifications have been with the iPhone almost since inception. If you want to disable those, go to the Settings app and then Notifications. Choose the app in question and disable all notifications. 

If you have disabled Background App Refresh, then that is set and it is disabled. There shouldn't be any need to do anything else and battery life will be maintained. Push notifications cause minimal battery loss and apply to all apps the same. As described above, you can disable those, still.