If it is not offline, it is not a back-up.
and how would you make 12hr back-ups on a offline(possibly remote) HDD?
The remote hard-drive can be in a system that stays offline until receiving a WOL packet.
I haven't got my routine backups working yet, so can't really tell you what I do.
Was planing to do both DVD-R HDD based backups.
Remote is important too. I suspect if your are using sneakernet, you would want to keep the off-site, off-line backups to weekly frequency.
Do your really have $600 worth of data every 12 hours? If that is the case, I may suggest some kind of version control system out of reach of the compromised Windows Machine.