The address that PufferPanel expects to be reached at is set during the installation when it asks for a domain. You cannot place PufferPanel inside a directory, but you can make a subdomain for it like panel.example.com and point that to your server. You will need to edit the server_name line in the /etc/nginx/sites-enabled/pufferpanel.conf (or /etc/nginx/conf.d/pufferpanel.conf on CentOS). You will likely need to re-run the installer (which will wipe out any existing data) or try the following command, which unfortunately does not seem to work for everyone. cd /srv/pufferpanel ./pufferpanel updatesite