Hi Anthony
Welcome to IW forums
I know backups have been talked about on the forums many times.
I think the easiest backup would be to use rsync and backup the required areas but we use R1soft.
Depending upon the quantity and space used, using IW backup routine could cause a higher loading. R1soft does not cause high load as rsync does not.
Have you considered your databases, both siteworx and IW. You would need to backup these as well
This link may help I hope for rsync and I think IW-Jenna posted a while ago over backup.pex, so perhaps open a support ticket
Many thanks
John