You can add a custom pak68.txt file for your mod, and ndmodloader will automatically load it, without the need to edit or replace the default pak68.txt file.
DO NOT include a full pak68.txt file. It will NOT work.

Example
- You have a mod, the archive is called coolmod.psarc
- The files in this mod require adding an actor to a level definition in pak68.txt, or the game will crash.
- You can create a file called coolmod-pak68.txt and include it with your mod (not inside the psarc file).

The structure is as follows (using example values, do not use these):
level-name some-level-name
actor some-actor-you-want
actor some-other-actor

That's it. That's the entire file.
Save it, and put it in the mod folder next to the psarc. When you launch the game, those actors will automatically be added to the some-level-name level definition.

Example mods that use custom pak68.txts properly:
Better Hairstyle for Savage Starlight Skin by gabedoesvp
Savage Starlight Black Outfit by Angel-gbc
Playable Owen (No Return) by gabedoesvp