It's cool. Currently I am restoring my iPod too. I jailbroke mine and the only thing I did was combine the video icon with the music icon to make 1 iPod icon like the iPhone. Quite the waste of work after all that work (at the time) I had to do to jailbreak it.
it can't hurt it at all (no way to brick a touch [sorta]) but it'd just make more sense to restore it in iTunes so you don't have any extra files wasting space on your iPod, or corrupting anything.