The readme file explains how to use the qualifier icons. You do it from the MFA file properties panel.
You'll be able to set percentage mode as default I'm sure. I can't remember which value to change off the top of my head, but it should be fairly self-evident if you look through the code comments.
I'm proud of my tools, but I've actually decided I won't do any more, as they take too much time away from Spryke.