The config in the ztpserver directory is the global config. The server has to be restarted to pick a config change up.
The config in the ztp-root describes the config of the server for provisioning.
Create folders in the nodes folder with the mac address of the device's management port. In this folder you can put the startup-config file, which the server will then distribute to this switch.
Keep in mind, that you need the bootstrap file under the bootstrap folder for everything to work.