Cool ideas. I know that I tend to just use a Journal file to correspond to a pdf if I'm going to do more writing that just marking up the page. And in theory, if I felt the need, I could just open the pdf on the LCD side and just have Journal open on the eink side. But usually I like to have the LCD for web stuff (looking stuff up or my twitter stream) while I'm "working" on the e-ink side, and I just use the button to switch between book and Journal.

But the horizontal split sounds both cool and useful!