How do I change NcFTPd so it doesnt create all those subdirectories when it logs?
You dont have to use the default logging specification (i.e. log-xfer=/var/log/ncftpd/%Y%m%d/@SETNAME@/xfer.%Y%m%d.%H). If you want just a single log directory, with daily logs rather than hourly logs, you just use something simpler, like log-xfer=/var/log/ncftpd/xfer.%Y%m%d. Repeat as desired with the misc and session logs. Also note that those cookies are just the same as you would use for date and strftime. See the man page for strftime to see what time and date cookies you have available.