I used the Super Mario RPG Music Mod from moddingofisaac to see if it would work.
I use ReiNX so my folder structure looks like this:
ReiNX > titles > Binding of Isaac TitleID (01005b9002312000 is the EU ID, 010021c000b6a000 is the JP / US ID) > romfs > all the mod files.
So, my full path...