PK3 files are normal zip files that we use in UFO:AI to organize the game data. You can add new files on your own containing your customized data. The pk3 files are loaded in order and doubled files will be taken from the last loaded pk3 file. That means that if you want to provide a mod for something, you can just overwrite a file that is also in another pk3 file and give your own modded pk3 files a name that is lexically ordered after the pk3 filename where the original file is included. Example: you can name your pk3 file Template:Path to ensure that is loaded after Template:Path.
You don't have to create pk3 files to add your modded files to the game! Files are not part of a pk3 file have a higher priority for the game. That means that if you extract a file from the pk3, modify it and don't put it back into the original pk3 - your changes will still be in the game and the original file is ignored. This also means that you only have to create a pk3 file if you want to do a release of your mod. If you plan to add your data (see License) officially into the game, you can even skip this step and just send us your files (included source files for e.g. sounds, textures [with layers] and map sources).
Let's assume you are planning to provide a script patch. You have two options here, provide a new file because you are providing new content, or override an existing file because you are patching existing stuff.
In both cases you have to create your pk3 file like this.
-ufos/ \-ui/ \- newUIScriptFile.ufo \- updatedAndAlreadyExistingScriptFile.ufo
In the case you are only providing new content you can name your pk3 file whatever you want. In the case you are providing updated content you have to ensure that the existing content is overridden. This can be achieved by choosing a pk3 file name that is lexically ordered after the pk3 file with the content you are trying to override. E.g. the content you are trying to override is in the Template:Path file - all you have to do is to name your pk3 file Template:Path. Every gamer that will now copy your pk3 file into this user directory (see FAQ) or into the game installation folder (if he is an administrator on his machine) can override the original content with your patched version.