I was using the File manager, and I did not understand the documentation very well. In case anyone has trouble doing this, use the terminal for CryptPad and copy the necessary file using:
cp /app/code/www/common/application_config_internal.js /app/data/customize/application_config.js
Then you can use the File manager to edit the application_config.js file. It is in the customize folder when you open the File manager 👍