What makes you think that there should be an ntp.conf file?
The configuration for time syncronization is the same as always. The fact that the underlying time-keeping software may now be a real ntpd instead of the old java hack doesn't mean the documentation for the system suddenly became worthless. Just add some servers, set the protocol (think only ntp works), and turn it on.
The ordering of the servers is something that I am not sure is of any consequence.
I'm not entirely sure what you mean by "the information"
"options" settings are kept in a file (actually a number of files) in the /etc directory on the filer. These files are not meant to be edited. Manual changes to the files will be overwritten unless you are running in a limited operating mode.
Your NTP problems are most likely fixed in 8.0.1P3.
ONTap isn't a linux OS... in case that isn't apparent.