The root album is the topmost album of Gallery 2. It's more like a container for your own top-level albums than a normal album.
Gallery 2 organizes your albums in a hierarchical tree structure. At the root of this tree is the root album. The root album has your top-level albums and photos as children, your top-level albums can have photos and subalbums as children again, etc.
You can have an unlimited number of albums and you can have an unlimited number of levels of subalbums.
Most of the site-wide settings are in site admin. Album / item specific default values are stored per album / item and thus, you have to change the settings of your root album for such settings. Just browse to main.php / your root album and click Edit Album to set default values as thumbnail and resize size and other things.