The light logo version is just an other option for you to use in case you have a dark header background for some pages and want to use another (more visible) logo for them.
The type of header version can be selected for every page in the page’s General Settings > Page Options & Style. If you chose the dark header, then the light logo version will be shown. If light header is chosen, the dark logo version will show up.
However, this is totally your choice. You can use just one type of header and the same logo throw out the site.
