So we're trying a new folder setting right now, it might take awhile to move the files to the folders but please bare with it. If you could start sending the deviations to the folders with the name of the character, if there is none there comment and it'll be added! Now any character in another costume will go under their name; Snow Miku, Zatsune and Bottle Miku go under Miku. However Genderswaps do not, they go into Genderswaps.
The group folder is for any deviation with more than one different character in it. Teto's in the Utau folder as she's not an official Vocaloid. If you have any other questions ask away!