As a best practice, you should disable any automatic software updates in applications that are published to production instances. This will avoid interrupting your end users with pop-ups or other notifications about new available software updates.
Instead, you should manage updating your software by using the Frame Sandbox. When a new software update is available, manually install the update on your Sandbox, test it, and then publish it to your production instances. This approach lets you control exactly the time when new versions are rolled out and deployed to your end users -- and essentially removes end users from the updating process entirely.
Ultimately, this is a key advantage of delivering your applications via the web: you control the updates. And furthermore, you can update your software as often as you like, even daily, without impacting your end users at all (just as with native web apps).
Note that when you publish an update to your production instances, any users currently running a session will not be interrupted. Their sessions will continue on the current version until they end their session.