Hello !
Centre centre centre !
Otherwise the shocks work biased, and the U join will/may/can touch something either at rest or when the swing arm is fully extended or compressed.
As to measure the gap, use Allen wrenches to fit between the frame and the swing arm. Easy to have at hand and quite perfectly calibrated for the job.
Remember to measure again the centre AFTER the nuts had been torqued to spec. Sometimes, when the bearings set it changes.