Branding Presets include font face and color choices, acting as your defaults when working on relevant Kaboodle products. Metadata Presets contain author, title, et cetera data that can be applied to your media assets (example: ID3 data in MP3 audio files).
Here's an example. You're working on a new product - we'll say an Email Flyer - and choose one of the templates as a starting point. Instead of seeing the template exactly as it was created, you'll see your preferred fonts and colors already in place. This not only saves you time, it really helps you project and maintain a consistent image. You may not always want your presets to be used. In this case just uncheck the "Brand" checkbox and you'll see the stock version of the template ready to customize.
Both Branding and Metadata presets are in development. They should be available soon.