The output directory consists of four basic components. The Shot Name, Suffix, Separator and Root Folder. The default root is //Output which is relative to the open .blend file.
The default separator is "_" which will be used to join filenames throughout the add-on.
The default structure is Root\ShotSubFolder\Filename
In detail; Root\ShotName\ShotName+Separator+Suffix
Some components including Suffix and Shot subfolders can negated, just beware that they can prevent files from overwriting eachother.
Redirect Main Output offers an alternative root folder that only applies to the scene output and is not used by output nodes.
The resulting file path is applied to the scene's output path and is updated when a shot is activated.
That's all there is to know regarding the default output file structure. For fully customisable paths, the next module has you covered.