So in effect, lets just say your SSD drive fails. As you are currently setup, can you boot from your secondary drive to your backed up OSX, or do you have to have restore that backup image to a new hard drive?
My whole rational of keeping the home dir separate (disk) from the boot dir is that I can switch among any number of boot drives any time I want to. For example, as a hypothetical case*, I use 10.6.5, and I want to update to 10.6.6, 10.6.7, or 10.6.8, I just do it to my ssd. Now I can still boot from my 10.6.5 backup, say for the sake of comparison to some weird behavior I see on the update, without a blink of the eye. I'm still using my same (common) home dir because it is not involved with the update. If I want to go "back" I can restore the ssd from my 10.6.5 backup.
Of course I would actually do it the other way and boot and update from the backup leaving the ssd alone (don't want to write to it any more than I have to). Only if I was satisfied with the new OS on the backup would I then update my ssd.
The point of all this is keeping the home dir off the boot dir allows you to "flit", "jump", switch, whatever, to different OSs (or backups of the same OS) at will. Your home dir is none the wiser unless the OS dramatically changes or screws things up (so that's why this technique may or may not work across major OS revisions -- Snow Leopard to Lion for example, but its great with a single OS sequence).
While everyone always debates the pros and cons of keeping the home dir separate from the boot dir, what always seems to get lost or not mentioned is the benefit of being able to switch among the OSs when they are separate.
So all of this was a long way of answering your question -- no you don't have to backup to the original boot drive before using it. Just boot from the backup. Your home dir couldn't care less.
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* For me going to 10.6.6, .7., .8 is hypothetical since I use 10.6.5 and have no current plans of updating beyond that (can you say "app store"? -- don't want it my machine -- and I won't debate any comments on this -- its my personal decision. And besides this is off topic.).