1. Obtain your app's current version from config.xml (search plugins on Cordova repo)
2. Fetch the currently available version via XHR. Simplest way is to have a JSON file sitting out on your server that you update each time the app is released.
3. Compare the currently available version and the app's current version. If they don't match, let the user know, and provide a link to the App store version.
This is assuming you just want to direct users to the app store whenever a new version is released. If you want to do code pushes, that's a different story.