Thanks for the thought on layers. We're hoping to add more shapes/images to the left hand side including things like icons so I hope it'll make more sense then. With the current set of mostly pre-made badge SVGs you're absolutely right!
In terms of making money, we provide a badging and certification service at https://www.accredible.com. We're aiming to keep this tool free so that it can be useful to people getting started. It's something we want to keep improving and it seems a shame to lock it down to our customer-base.
I'm not sure if clicking a badge should add them on top of the existing layer though - would many people design complex badges? If not, maybe save the current badge and let users see the new badge they click from the left instead of the current one.
How do you plan to make money from this - appears to be completely free to make and use the badges. I had a brief look at the help (which probably shouldn't be on a different domain), and didn't see much there.