Many shafts have keyways cut into them to hold the coupling. “Keys” are pieces of square metal stock inserted to hold the hub in place.
If there are two (2) keys, one on each side of the coupling, you should not “align” the keys across the coupling. Instead, it is very important to ensure the coupling mass is balanced during installation. The mass of a key is balanced by setting the two keys 180 degrees apart from each other. If the keys are set on the same side, the coupling will induce a mass unbalance situation.
Often a vibration report will note a misalignment condition, but precision alignment techniques will not find any issue. This can lead to friction between the vibration analyst and the millwright. Keep the keyways 180 degrees apart. You will help improve the life of the coupling and keep the vibration low.