I place my calibration mike right where the space between my ears will be (yes, the space is probably empty). However, this only works well for solo listening. In the Theater room, I took several measurements and struck an average, then measured again and made tweaks.
However, I am using a pure analog approach and imagine the automated software in your pre/pro will adjust for some of what I do manually.
Pepe, I do agree calibration mic placement makes a big difference in how things turn out and experimentation is the way to the best outcome. Most of the rooms I have measured take a few attempts before I am satisfied. When your ears like the result, you are done.