Try using a monitor arm and angle that monitor in such a way at such a height, that you would not have to adjust your head along the vertical axis. It only works with monitors up to a certain size, though, which is the biggest limitation.
Actually, my lower monitor is my primary monitor for my desktop PC. But for a while, I used a similar setup with a Thinkpad as my lower monitor and that worked just fine for me too even though I used the large upper monitor as the primary monitor then.
