I have used the system notification plugin from the github(https://github.com/saileshmittal/phonegap-system-notification-plugin) for android phonegap.I have used this code in my
According to the phonegap documentation you cannot run the apps in the background, the js cannot continue to run. The reason notifications are able to work is because they are using the native system to send the notifications.
In order to make processes run in the background you will need to create a plugin that uses the native os.