Two things that matter as much as position and get set once and never revisited.
Distance. Further away than most people sit. A common guide is roughly an arm's length from the screen, and further for a larger one. Sitting too close is a large contributor to eye strain and to the head-forward posture that produces neck ache, and with two screens it also makes the turn to the second one much bigger, because the angle grows as you get closer.
Moving both screens back ten centimetres often does more than repositioning them.
Height. Top of the screen at or slightly below eye level, so your gaze runs slightly downward. Both screens at the same height if they are side by side: a mismatch of a few centimetres means a small head tilt every time you look across, all day.
And if you wear varifocals, all of the above changes: the reading portion is at the bottom, so a screen at standard height makes you tilt your head back to see it. Lower is usually right, and it is worth mentioning at your next eye test since there are lenses made for this.
On your existing ache: give a changed setup a couple of weeks. It will feel wrong at first because you have adapted to the old one, and that is not a sign it is incorrect.