I want to put up chair rail in a room in my house. However, the windows that are in the room are at two different heights. Where should I place the chair rail since I can't evenly butt it up to the windows?

How much diff in heights?

Adjust it to hit both windows and or below the windows which may show more of a height diff by the eye. If it broken up by the windows openings then its less for the eye to catch.