jwz mentions PSA: Backups a backup system that's fairly clever. Your backup method is to essentially restore to the replacement drive. This seems to work simply on OSX. What all do I need to do to adopt this guide to Ubuntu?
Answer
Partition the two external drives the same way as your system drive, and rsync all your partitions as well as dding the boot sector (the first sector of the drive) from the system drive to the external drives. Ugly, but serviceable, if you get your partitioning right (big if).
Also take a look at more advanced "system snapshot" systems like mondo rescue, which kinda take care of that sort of trickery for you.
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