I think you should ext3 format your drive (or at least make a ext3 partition on it) and copy there your / . (just doing this shouldn't destroy your drive!
I'd recommend use the cp command, see 'man cp' ...
you could make an script to backup automatically.
to manage partitions gparted is a good program. if you'd rather just format all the disk, 'mkfs.ext3' would be the way to go.