I hate to say it but it's all about practice. Play a bunch of practice rounds and just get to the green and put yourself in different positions so you can see how the bal reacts to the undulations, ridges and "intangibles" like drift. Even the perfectly hit putts seem to drift a bit. Odd but true.
One thing which helped improve my putting immensely was aiming and putting from the reverse view...give it a try if you haven't already.