What you need:
Smash 3DS romfs (braindump is the best way to do this)
PackHack (download
here)
A hex editor (I use HxD)
Any nus3bank file (easily obtainable from BrawlCustomMusic)
1. Extract romfs.bin from braindump using the "RomFS Extractor.exe" available in the Pack Hack. This will create a folder called "romfs_" wherever your romfs file was.
2. Navigate to "/romfs_/sound/bgm/". Here you have all the stage music from the game in the nus3bank format. Drop your custom nus3bank file here, making sure that it has the same filename as the song you are replacing.
3. After you have replaced any songs you want, run "RomFS Builder.exe" from the Pack Hack and pointing it at your "romfs_" folder. It will ask to export a file. Name this file "[last 8 digits of gameid].romfs". Smash 3DS is "000edf00.romfs".
4. Now that you have a new romfs, load this file into your hex editor and delete the header. In HxD, press ctrl+e and in the end-offset box, type FFF. Then press the delete key on your keyboard. Press okay to confirm the deletion.
5. Now place your *.romfs file into "/hans/" on the root of your 3ds sd card. If you have followed all the instructions, Smash 3DS should load the custom music on the respective stages.
Haven't worked out getting updates to work, but I'm willing to bet that putting the update data in the romfs will work. Haven't had the time today to test anything. If anyone has any questions, feel free to ask me. This was a quick guide, so I apologize for any mistakes.