@alturis I'm not fully sure about the theming aspects of it, and how that's structured.
The custom-collection theme folder has the theme settings for all the custom collections that will be grouped under the "my collections" err... collection, as sub-folders.
You won't be able to further customize them there - there is a single theme/layout for each ES "system".
If, however, you're looking to add specific custom collection artwork, add them to the root of the theme. Look at some of the other custom collections (mario, kids, shmups) in that theme for a good example. These will show at the main carousel level, though, not inside the "My Collections" folder.