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Measure eye to eye because you're trying to measure sag as a percentage or length of what the shock's full stroke is.
measuring from fixed points, a fixed point to the top of the shock eye, etc. wont get you an accurate measurement unless you like figuring a few more Pythagorean theorem problems out as well.
The pros do it this way.
And, I suggest that when you sit on your bike for the final measure, you should be in your "Attack" pose, not just sitting there upright like a sack of potatoes!
I agree with others in that it doesn't matter what is used, as long as your consistent. You're measuring SAG based on the actual stroke length of the shock and thus taking that SAG portion from the length you're measuring with, be it from bolt center or wherever.
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