So what you need to do (if I understand your use case correctly) is have a popup.js and popup.html which will handle user interaction and will send messages to the background.js background script that will register the Alarm event handler.
So what you need to do (if I understand your use case correctly) is have a popup.js and popup.html which will handle user interaction and will send messages to the background.js background script that will register the Alarm event handler.