I've always stacked my monitors because I recline while I work, so the up/down eye motion feels natural for me. By contrast, I turn my head to see side-by-side monitors, which doesn't feel as nice to do all day.
Can you elaborate on this? Sounds like it might be a way to limit back strain? Do you have a desk at all?
For me, this totally eliminates back strain from working. I've also got a friend who uses a La-Z-Boy in his home office, with his laptop connected to the TV. He can't say enough good things about that setup.