Check out my scrolling doc on the main page. At the end of the document, it discusses how to update the scroll registers to any value on the fly, by alternating writes between $2005 & $2006.

And BTW Memblers, the way that was done in Bigfoot, according to Andrew's post on the mailing list a couple of years ago, was that he basically waited for the appropriate scanline to make a dual write out to $2006. Since the write cause the fine- v scroll to be reset to 0, you can see why it effectively allowed smooth vertical split screen scrolling.