for a complete and bootable copy of your main hdd, i suggest you setup a raid1 mirror. basically, the 2nd hdd will be an exact replica of the 1st/main hdd. if your 1st hdd dies, the 2nd hdd will automagically take over.
note that this IS NOT a backup solution. if you want backups, you will need something like amanda (for daily, weekly, monthly backups), or rdiff-backup (but u will need to bake your own scripts based on your needs).