The optimal setting for everything is to have the jack plate centered in its up/down travel, as that is the point of maximum mechanical stability. Some jack plates use contact between the two sliding plates for stability (hydraulic plates fit here for certain). Most mechanical plates use bolts on the side that clamp the two pieces of the plate together when they are tight, you loosen those before you can raise/lower the motor. If you have the latter type, which holes you use don’t mean a thing. If you have a hydraulic plate, it is best to mount the motor so that the optimum engine height has the jack plate centered in its travel range to spread the pressue over all of the sliding contact points…
Hope that helps…
My $.02…