I used a dry erase marker and a really long straight edge on mine ... put a straight edge up against the lower part of your transom and trace the line to each side, then mark the center of that line. Measure 8-12 inches down from each corner of the lowered transom and trace another line from side to side passing through each mark ... mark the center of each line and trace one line going down ...
I'm use to marking centers of rooms & portions of rooms with chalk lines. Can't ever count on straight or plumb walls. I use a lot of what I learned in high school geometry. Comes in handy to see everything snapped out in bright chalk before you start cutting and drilling.