This guy has it figured out. If your scope is FFP, look at the correction on the reticle and apply that to your turret, if the scope is SFP then crank it to the predetermined magnification level (most often max power) and treat it like a FFP. I NEVER think of corrections in inches or centimetres, I use MRAD for all my target scopes so I think of my corrections in mils (MRAD=mils, not mm).
If you have to think in inches or cm, use this...1 MRAD is 1/1000 of the distance to your target REGARDLESS of the unit of measure. So you are sitting at 1000 metres, one MRAD is 1 metre, most scopes in MRAD use a 1/10th click adjust so one click is equal to 1/10th of 1 metre, or 10cm, at 1000 metres. If you prefer yards then one MRAD is 1 yard or 36 inches, one click is 1/10th or 3.6 inches. But I question why you would do this when the ruler in front of you eye (reticle) is either in MRAD or MOA, so why say it looks like it is 5.5inches low? Use the ruler (reticle) and measure it in the units of the ruler-either MRAD or MOA and apply that correction to your turret. It is so easy even I can do it.