Basically you want to trigger a countdown on your extension from your backend or the configuration view?
If you want to send real time messages you can use the extension pubsub https://dev.twitch.tv/docs/extensions/reference/#send-extension-pubsub-message
And use the listen methods from the javascript helper to get the message sent by your server and call your javascript function on your frontend https://dev.twitch.tv/docs/extensions/reference/#helper-extensions