When setting sag you need to start from a fully extended suspension. Part of the total sag dimension is the amount of sag just due to the weight of the bike without rider, passenger, or luggage. Let's say you're installing shocks that have a total travel of 3.0 inches, and you've decided (or been told by the manufacturer) that a good sag number for your situation is 1.2 inches of shock travel. Rather than try to make accurate measurements from the fender to the ground, I'd suggest measuring the shock when fully extended from eye to eye, then measuring from eye to eye when loaded and adjusting the preload setting until you get the 3.0" minus 1.2" dimension (example only, your numbers will vary). You can rig up a simple jig to make the measurement easier, like with a straight bar or plastic pipe with a right angle fitting on one end that will fit snugly over the shock nut and another at the correct center to center distance you want. Adjust until both ends will slip over the upper and lower nuts. I wouldn't be surprised if someone has actually developed a similar tool just for this purpose.
Jerry