How to configure spare Hard Drive

I have two 20Gig hard drives.

I want to use one for general use and the other for saving back up documents
and programs. But I also want to be able to boot up on either one. In fact,
I'd like to work it so that the backup will be a mirror image of the first
drive. If that needs special software, then I'd just like to use it for
backing up.

So I uncabled the second drive and formatted the first drive (DR0) to boot
up for general use.
Then I moved the cable (DR0) from the first drive to the second drive
(careful to change the second drive's jumper to make it DR0) and formatted
it the same way.

But when I change the jumper back and hook them both up in their original
configuration as DR0 and DR1 on the same cable, the second drive
automatically gets reformatted somehow and I lose the system boot up stuff.

What am I doing wrong?

Thanks in advance