MobiOne applications are not configurable to run in the background. Thus, an internal timer is only reliable when the app is active.
If you need to notify the user of some event or state while the app is running your app has access to the Cordova javascript notification apis (vibrate, alert, prompt…)
See this link for more details http://docs.phonegap.com/en/2.9.0/cordova_notification_notification.md.html#Notification
Your timer (e.g., setTimer() or setInterval()) can call any of these notification apis when needed.
We recommend placing the code in the project’s www/<startupfile>_custom.js file or a separate js file and adding it to the project as an addition javascript file. (hope this makes sense)