I have struggled with leaving putts short, then blasting the next one way past. Part of my problem was really with my stroke; it was okay for short putts but I couldn't seem to add incremental power to it very easily. I've been working on that aspect and continue to do so.
Swapping to a putter that gave me a bit more feedback than my Odyssey seems to have helped too, although I suspect that simply spending more time on the practice green is what has done the most good. Putting is all about feel, and I don't know any way to develop feel than by practice. Whether it be putting or the short pitch shots around the green, practice may not make perfect, but it will almost certainly make better.