From what I've tried, you can put the files from the BMDS_whatever folder in its own folder on your card, then unzip an place all of the wavs in the same folder:

Root
->BMDS
-->BMDS.nds
-->BMDS_touch.nds
-->bokudora.bms
-->oharock.bms
-->anpanman.bms
-->-1do.wav
-->-1do#.wav
-->-1fa.wav
-->-1fa#.wav
...
...
...

^like that.

The songs work fine when I place them like this. Try this setup and see if it works.