Before you blame your putting stroke for every three-putt, take a closer look at your short game—in particular, your chipping and wedge play. If the average length of your first putt is greater than 20 feet, you're not hitting your short shots close enough to the hole, which puts a ton of stress on your putting game. Work on the following chipping drill in practice and you should quickly be able to cut your leave distance to under 10 feet, which will make two-putts a whole lot easier.
First, lay your golf bag down about 18 inches in front of your ball, and without allowing the club to touch the bag, hit some chips over it with your sand wedge. The close proximity of the bag will force you to hit down on the ball sharply and with lots of acceleration, creating spin and giving you good distance control. You'll also learn to keep your weight forward and your hands ahead of the ball at impact, which is key to hitting solid chips and pitches and eliminating those lengthy first putts.