I think you would split the difference equally to both ends of cut shaft. let's say implement is higher or lower due to terrain or tractor pto shaft elevation higher or lower due to the same. Remember is the shaft is not cut short enough and you have a heavy implment like a tiller and if you lower and hit a bump then then energy (potential and Kinetic) would be against the tractor rear and PTO final shaft. It could potentially bust the rear housing, damage the pto and seal there. You also need good inner and outer cut shaft overlap for good torque transfer.