I'll do my best to explain:
So the first thing I used was
this tutorial to extract files and get the exefs.bin. Make sure you can see hidden file extensions (as the problem with mine was that I had named it exefs.bin.bin on accident).
Anyways once you've used the hackpack to extract a decrypted 3ds file (I just used rx tools) you will be left with decryptedExeFS.bin (also, and forgive me here but I
believe that I chose to decrypt "code.bin" in the extractor, but I'm writing this quick so I don't have time to double check ATM). Make a copy of that and put in the workdir folder from the layeredfs zip file you can download
here.
Make sure you have it named exefs.bin. There also should have been a folder called exe that was created when you extracted your rom. Rename this folder to exefs and put that in the workdir folder as well. Double click the buildlayeredfs.bat and when it gets to a point where it asks for an sd folder just type something game specific, i.e. "smashbros" and hit enter.
If everything worked right there should be a file in the workdir called layeredfs.plg. Now on the sd card you need to make a folder called "plugin" and inside that a folder that uses the title id (0004000000125500 for Majoras Mask for example, I just used FBI to look at the I.D. of my installed cia's). Inside that folder is where you put your layeredfs.plg.
The last thing you will need is the folder name you entered when you ran layeredfs.bat, which in this example case was smashbros. Inside that folder, match the way the folders were in the romfs when you extracted the rom (example: if romfs/sound/stream/<list of sound files> then the sd card would have smashbros/sound/stream/<your edited files>.
If it was all done correctly then when you run your game using ntr it should flash green very quickly and then the game should start. I will write a more in depth post later/edit this one later today.
Also if anyone is interested I can share the edited files for Majora's Mask.
Edit: Will be trying this with Smash Bros in a little while too so I can make a more personalized tutorial on that game alone.