The only NTP-related GUI settings are on the System -> Settings tab, where you can enter up to three timeservers.
If you want to add additional settings to /etc/ntp.conf, you'll need to hack /etc/rc.d/ix-ntpd (applying the changes to /conf/base/etc/rc.d/ix-ntpd to make them permanent) as it is ix-ntpd that writes out /etc/ntp.conf from scratch each the ntpd service is started... You can also create the additional file from within ix-ntpd. I'm really not sure why there is an ntp.conf at all in /conf/base/etc, as it's ignored.