That's correct. The Config tool cannot currently setup a dual z axis. That must be done manually in config.g.
The config.json file is not editable either. It's simply used to bring the config from the tool back into the tool in case you wanted to make a change or use it as a base to modify from.
For the part cooling fan you can click on the fan0/fan1 boxes for each tool to assign them, in case that wasn't clear.