ROM Hack VVVVVV 3DS Custom Levels by adding files into the CIA, how do?

[KapuDaKoopa]

Hello everyone!
I have a VVVVVV 3DS CIA, and I can install it and everything. It works normally.
Now, I understand you can actually add custom levels to it using the homebrew apps braindump and HANs.
I can not use either of these, as my 3DS breaks when trying to use them.
So I was wondering:
Could I extract and decrypt the CIA, add the custom levels and encrypt them again, and how would I go about doing this?

EDIT: Also, some levels use custom graphics.
Where would I put those?

EDIT2: Nevermind, I think I've started to figure things out!