Becky:
if you are having knee pain, yoga will not specifically get rid of it for you. You need to ensure that you are not developing muscle imbalances through your running training. You need strong quads, particularly along the inside of the leg and a balance of strength between front and back of leg, between quads and hamstrings. Check your glute strength also: the glutes are 3 muscles and sometimes the gluteus maximus gets all the work. The minimus may need more strengthening. All of these factors can influence the riding/sliding motion of the knee cap which can cause knee pain if it is being pulled out of alignment.
I would check with runnersworld.com for specific exercises to help prevent knee problems. They include whole sets of core exercises specific for runners.
As far as core strengthening is concerned, you are much better off with pilates than yoga as pilates works the deep lying abdominal muscles better than any other exercise type.
Clare