Like all things golf, its about putting (haha) in the time for practice. From what I have heard some people take their own notes, and probably the majority base their putting on familiarity. If you play this game enough, you will probably see the hole from every angle at a certain point, so a lot of it can be memory. Hole 3 on Kiawah for example. Left of flag about 6 to 15 ft away, I know that putt, cause I get it so often. Perhaps the best way is to hit to your familiar spots. Pro's dont aim to be above the hole with a nasty slider, they aim for the flat putt, or uphill putt. Hole 2 on Kiawah, usually have between 50-60 yards to pin, I always try to either be on the hole or right of the hole, which gives an uphill putt. I never want to be short or long because that leaves that 2 ft breaker many hate.
So my rule of thumb, become familiar with the greens, try to stay under the hole, and take notice of how much certain holes break. Example Hole 5 on Kiawah, very hard to keep it less than 7yds left of the pin, even landing short right of the pin, that putt never breaks as much as I would line it up for, so I cut it in half, add another ft or 2 in speed and let it go. Have made some good birdies last couple of days. Same on #4 of Kiawah, I stopped going for the flag, instead try to be on top of the mound or just past it, and that putt I make 50% of the time now.