runDatagen deleting my custom json files

I'm currently learning, or following on Kaupenjoe's Fabric 1.20.1, Mod tutorials and I got the gist of how blocks are created etc. But I have special cases where I don't know how to write in blocks with specific cases like overlays, or ones with side bottom top textures into the java files themselves so I opt in to write it manually and place it in the assets folder. But everytime I run Data gen my written json files disappear and the json files generated by the Model Generator remain. Can someone give me an in depth guide on how to create specific blocks on the Model Generator or a just a way to stop it from deleting my json files.