The way I see it: playing by folder limits the available tracks to the files in a folder.
If that is not the desired way, it would be another approach to check if the player also interprets tag data (filenames are not really tags).
A good way would be to fill the tag fields ALBUMARTIST, ARTIST, ALBUM, TITLE and TRACK.
If you could check how files behave with this metadata, it would be easier to adapt the data to make it play you want it.
See also this thread about problems with a car stereo:
Or this one for different sorting options in a player (not necessarily features of your player)