For Higan, you need to name the file as follows:
ROM file: "program.rom" (this would be something like "mmx.sfc" or "mmx.smc" originally)
MSU file: "msu1.rom" (this is just a blank pointer file to let Higan know it's a MSU game)
PCM files: "track-1.pcm" ... "track-65.pcm"
If a save file is included with the patch: "save.rom"
Do NOT include a "manifest.bml" or "manifest.xml" file.
You do have the PCM files, right? There's usually a download link for the PCM files in the readme included with the patch.
If it doesn't have a link to the PCM files, check here: https://www.zeldix.net/t1265-fixing-all-of-the-too-loud-audio-packs-for-good?highlight=fixed+audio
for a PCM pack for your game. There are two pcm packs for mmx there.
There's also a pack for MMX that's all the MMX tracks processed through a Genesis sound chip and converted to PCM here: http://www.romhacking.net/forum/index.php?topic=24980.msg344955#msg344955
PCM packs are interchangeable with the same MSU-1 patch, so you don't need to re-patch the ROM for each audio pack.
Alternately, you could try using this: https://dl.qwertymodo.com/snes9x.zip
It's Qwertymodo's build of Snes9x with MSU-1 support (which will be included in the official build of Snes9x whenever they get around to releasing v1.55).
The file structure for that is:
ROM file: [rom name].sfc
MSU file: [rom name].msu
PCM files: [rom name]-1.pcm ... [rom name]-65.pcm
If a save file is included with the patch: [rom name].srm
Again, do NOT include any xml or bml files. This is the file name naming scheme as SD2SNES.