I hope you're not asking me I haven't got a clue. But I suppose uploading it directly to the skin's folder would be ok since the header image shouldn't be updated in a long while.
Since I need to translate any new skin entries as the updates roll in, I have to tar everything up and upload it anyways. I never really thought about your situation.
My understanding is that anything in the skin folder can be updated at any time; I have no idea if an entire skin is uploaded or just the changed files.
But that's fine for admins. Resellers also need to change the header image, so they still need to import their personalized skin (by tarring and such) since they don't have root access.