The Main Index will, by default, show the logos of Beavers, Cubs and Scouts over a 'brand illustration'. They are linked using the URLs configured in the theme. The Logos are implemented as a separate module that can be loaded in to any page template as many times as you like but they are styled to work on the Main Index so they might not look quite right on other pages without additional work.
The Explorers logo can also be displayed and the brand illustration background is optional as strictly speaking it violates the exclusion zones of the logos.
It is also possible to show the Network logo (from version 3.4.6). With all five logos displayed they are left justified rather than spread out evenly.
New section logos have been introduced for 2015, and the old ones are due to be phased out by September 2015. These are supported from version 3.6.0 of the theme onwards, with the default initially being to use the old logos. The new logos have a greater combined width when displayed with the same height. This means that they need also to be left justified when there are four logos and they have to be displayed in different sizes depending on how many are displayed. As they are essentially text based logos they wouldn't really work if they were given transparent backgrounds and arguably they don't work all that well when overlaid over the brand illustration.