Updates have two different scenarios - 1) Server driven updates where you don't need to modify your code. In this case your App should be intelligent enough to poll server for any updates, download them, and reconfigured itself. I am doing this for our native Apps. And 2) You have updated the code. In this case you will need to re-install the App on each device to update it.
In your case I think you are looking for solution to scenario-2. You can implement something similar to what Apple does when you submit updated version to Appstore. They display updated apps in Updates section and you re-install the App. You can have some section in your app that check if there is an updates and calls itunes service with your HTML link which will directly give pop-up to users asking for installing updated app. Second option you can use Push notification after you have updated .ipa and .plist file with updated version information.