That's normal empeg behaviour: if you have a hierarchy of directories containing music, just drag everything to the place in empeg's playlist structure you want it. Say you have 'Artists' list in empeg, and 'Pink Floyd' directory on PC, with subdirectories for each album, 'The Wall' having subdirs for soundtrack and 'regular' album (and even perhaps 'Disc 1' and 'Disc 2' subdirs below). If you drag 'Pink Floyd' dir into 'Artists' playlist, the whole hierarchy of playlists will be created, and tunes downloaded.

If you somehow manage to delete playlists on the empeg while tunes survive, the fastest way is probably deleting tunes as well and draging everything from the PC anew. Of course, to do that you have to actually have your tunes on PC (or off-line, on CD-Rs, tape or similar); it will also be nice if you tidied up your ID3 tags before uploading.