If you're going to buy this much disk, why don't you consider some form of hardware RAID (Redundant Array of Inexpensive Disks for those who are not so IT literate). I believe they're a lot cheaper than they used to be.I explained my plan poorly - I planned to buys 2 500's to give me a terrabyte in total. I wasn't intending to buy a TB and partition it into 500 X 2.
The pluses---you get more usable disk space, e.g. 5 * 200GB disks makes one 800GB RAID5 array, and it will survive the death of one disk; also you wouldn't have to backup everything from one disk to the other.
The downside, reading and writing to a RAID5 is slower, but I can't believe you would notice with the uses you will be putting it to.
What you are suggesting is in effect a RAID1 mirror, except you are doing the mirroring manually. This is obviously safer and faster, but more expensive per GB as you lose 50% of your disk space, since one disk is literally a copy of the other.
It all depends on how much you're willing to spend to protect your data. But I would copy them off to CD/DVD as often as possible, even if it means wasting space on the CD.