To use custom pk3: place them in "gamedata\base" folder of your game.
If you need to make your own Pk3's you should know the game uses a default dir structure for every asset in the game. Open the assets files in gamedata\base\ for a better idea.
Usually starts with the category and then a sub-dir for level, character, weapon, etc.
So when comes time for packing everything, you need to follow these guidelines.