So, pk3s work fine now. Not sure exactly why it wasn't working before; perhaps I had the directories set up wrong, who knows.
I do have some other questions, though I'm not sure if I should start a new topic for them:
First, I want to include custom music with the pk3.
Second, I will need some guidance in making SHADER files for various custom textures; I have no idea where to even start with this (yes, I've looked at the official online documentation for shaders by Icculus, it makes no sense to me).
If anyone can help or at the very least point me in the right direction, it would be much appreciated.