Sorry for not responding sooner Peter but we just got back from vacation...
When making a guitar, I establish a center line on the body (and neck) on the blank stock. If I am gluing up two pieces for the body, I usually make the glue line the center line. That way it's easy to find throughout the process. For the neck, I mark front and back as well as the top and bottom edges and remark the line when I lose it through the profiling, sanding, etc.
For an existing body, I use the center of the neck cavity and, if possible, the center of the bridge or tremolo. A fixed bridge will have screw holes and you can measure the distance between them for center. A tremolo thru-cavity is off center but you can use the center of the spring cavity on the back side and follow that through the thru-cavity. To double check, I'll mark the centers of the pickup cavities and place a straight-edge along those and the other two marks (neck and trem) see how they all line up.