Hi Etneural,
The auto-configuration tool is not something that can easily be customized since this was created as a secondary 'helper' tool. Is there any reason you are not configuring your camera(s) directly to upload to CameraFTP? This is the standard way of using CameraFTP: Access your camera configuration pages and fill out your CameraFTP credentials to have the camera upload directly.
Please email support@cameraftp.com with any other specific questions about the configuration process and we can certainly help troubleshoot more comprehensively.
Best,
CameraFTP Support