If you’re running spring cups/seats that the damper would be contacting, then I’d run that end down.
If they’re stock heads that still have the factory locator step, and the damper would be sitting on that step, I’d run the “small end” up.
Edit....... I misread the question.
As far as the damper being high or low...... makes no difference.
They will equalize out during operation.
Also I cant find any clarification when checking installed height, do you included the seat locator in the measurement?