Depending on your requirement I usually don't want to have a lot of different folders in the root of the website.
So I usually make sure everything is stored in a /media/ folder, and when multi site I add the /sitename/.
When using full url's remember that the path will show.
So the url of an image that lives on media lib site A
will be something like www.siteB.com/media/siteA/somefolder/someimage.jpg
I can imagine some clients don't want the name of siteA in the source of SiteB.