You just define two portions of the screen (one 'scroll slow' part and other 'scroll fast' part) divided horizontally. Then you set up the VDC's Raster Counter to the scanline # correspondent to your desired horizontal split.
Then it's easy, only thing that changes is that you write to the Scroll X register twice, once for the top part in the beginning of the picture rendering (VBlank) and again inside the IRQ interrupt handler (fires when the line being rendered matches your configuration for the raster counter registre). That way you can have individual scrolling speeds for each section of the screen.
edit: of course there are other, more complex tricks (like dynamic tiles, used in Ninja Spirit) and you could also set up some sprites to help mask the horizontal divide (like atlantean, some parts of the walls that stick out outside of the horizontal split are just sprites). And of course, I really don't know how this works at all in HuC so hopefully my confusing post was of use.
