Branding Presets include font face and color choices, acting as your defaults when working on relevant Kaboodle products.  Media 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 a 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 where appropriate.  This gives you a head start on making the Flyer truly yours.  (Now, 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.)