The first thing I did was to make marks on the front & back of the bike so I knew how tall the bike was stock. Then, I sat on the bike and measured it's height with me on it. This step tells me how much the bike will "sag" with me on it.
After it's lowered, I'll check the two measurements again. The instructions tell you how much it should sag when you're done. If the sag is wrong, you adjust the clickers on the back shock.
Oh, since the links only lower the back, I'll have to loosen the bolts on the forks and slide the forks in the triple clamps to lower the front. That's why I measured the front and the rear of the bike: so that it will be "level" when I'm done.
Here's a picture of me measuring how tall the front of the bike is and a pic of the rear.
On the front, I measured the total height of the triple clamps & I also took a measurement of how much the forks stick up out of the clamps when stock. This way, I know how tall the front is compared to the rear and I also know the stock settings if I ever want to set it back.
On the rear of the bike, I measured from the tape mark to the axle.