There are no folders on empeg, just tunes and playlists. Tune files are all in a single directory (you don't see it). What you see are playlists and (depending on SW release) 'soup views', i.e. pseudoplaylists constructed from tags (by author, album etc). So, say you create a playlist 'Singles'. You can add to it whenever you rip a new single; you can also link the same tunes to some other playlist (say, by author, genre, remixer etc).

See what FAQ on riocar.org says on that (and on other themes - skim it at least; even better, read it, it's good reading material)