You will probably want to enable a cronjob for backupninja to do its job. 

This is the default builtin cronjob:

# /etc/cron.d/backupninja -- cron tab entry for package backupninja

PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin

# run backupninja every hour on the hour
0 * * * * root if [ -x %%PREFIX%%/sbin/backupninja ]; then %%PREFIX%%/sbin/backupninja; fi

You will also probably want to configure log rotation on the
/var/log/backupninja.log file.

Finally, note that ssh-copy-id isn't available under freebsd so part of the
work done by the ninjahelper(1) wizard won't work and you might have problems
configuring backup schemes using that. You have to manually copy the SSH public
keys for the backups to work.