Have you noticed anything new when using FTP?
To date you were able to update web pages and other assets such as images, scripts, css files and so forth. Now you'll notice the addition of 2 new folders called Templates and Layouts.
Using FTP you can now add, update or delete Site-Wide templates. You can also download and make changes to any of your module layouts. To see these changes simply connect to your website using FTP and look out for these 2 new folders.