Thanks @Phaedrux! that's just what I needed. I created a cronjob to run the following script every hour while I'm trying to get things running.
now=`date +'%F_%H.%M.%S'`
host_address="username@host"
filename="[backup file pathway]/$now/"
#echo $now
#echo $host_address
#echo $filename
ssh $host_address mkdir -p $filename
rsync -av /opt/dsf/sd/sys $host_address:$filename
rsync -av /opt/dsf/sd/macros $host_address:$filename
The script above requires automatic ssh login, a good link to set that up is here: http://www.linuxproblem.org/art_9.html
Cron:
# m h dom mon dow command
0 * * * * bash /home/pi/Documents/backup-duet3.sh