Epson recommends emulsion side (dull) up for the V700. Some users (myself included) have found that they have less film curl/sag problems with the Epson 120 film holder if they mount the film emulsion side down. Still others report better results in general for 35mm film with the emulsion down. Hard to say which is best, though emulsion up will yield correct orientation without the need to flip in PP.
BTW...Nikon recommends backing side (shiny) side up for the Coolscan 5000. This is also the general rule for optical enlarging. The old darkroom adage is "shiny side up" for both film and paper
Steve