The FreeNAS GUI have the option of running nut as master or slave, so it should be no problem setting it up.
The problem comes when you have multiple (redundant) UPS'es, the GUI does not handle that well.
You could configure nut yourself, and either chflags schg /etc/local/nut/* to keep the freenas gui to mess with the config files.
Or change nut_prefix to /usr/local.myown in /etc/rc.conf.local and have the nut config files in /usr/local.myown/nut
As usual, the GUI is useful and easy, but if you really want to do serious stuff, you must use CLI.