First of all, I'm happy to see that that this plugin is still in development. I tried to comment on it in the past through code.google.com and the WordPress forums, but I got no reply. Or indeed any indication it was actually read by anyone.
I believe that the best layout would be either multi-page or (preferably) tabbed.
I think there should be at least three tabs/pages:
1. Presets (where you load/save/delete/import/export presets)
2. Preset Options (where you define the actual HTML and shortcodes for the currently loaded preset)
3. Preview (where -obviously- you see the a preview of the list)