Hi Phil,
Did you setup the push notification widget as described in the docs: https://docs.mendix.com/howto/mobile/native-remote-notifications#3-2-setting-up-a-notification-widget
This contains event handlers actions when someone clicks a notification (outside of your app) or when the notification is received and the application is open at that time. With the last one you trigger nanoflows or other actions and show a popup yourself!