I think (not sure) that if the M3Us are part of the same drag-n-drop operation, that the songs within would either be doubled as before, or they would be counted as duplicates.

If you want to maintain separate playlists, apart from the artist/album trees you've already got, then you really have to do it manually in emplode. There's no proper provision in Emplode for using M3U playlists on the PC as "soft" playlists on the player. They are treated like another directory entry from which to import files. (I believe I said this in that FAQ entry I linked.)

Yes, I want this feature, too. I know we've bugged Mike Schrag to add something like this to Jemplode, but I don't know how far he's gotten in that area.