SD2SNES/Snes9x Installation Final Notes
I don't have an SD2SNES, so I can't vouch for these directions. If you're testing on an SD2SNES, your feedback on this patch is vital, please report to me your success (or failure) immediately.
As far as I understand, the SD2SNES simply needs the .sfc file, an .msu file of the same name, and a series of .pcm files named sfcfilename-##.pcm where ## are track numbers. This is exactly what you should find in your destination directory. So you should just need to copy the contents of the destination directory onto your SD card and put it in your SD2SNES, and it should all work. Recent versions of Snes9x now have MSU support and work identically. Have fun!