"In box" Windows Home Server offers no functionality for backing up the system partition. Everything on that partition is sacrificial in the event of drive failure.
That said, your assumptions are good. I would not personally use SecondCopy, instead I would use robocopy (in box with Vista). But that's because I've used robocopy for many years, and I'm confortable with it. I don't have anything against SecondCopy except lack of familiarity...
I'm not on the WHS team, I just post a lot. :)