First question is, are your knees in line with your toes throughout the entire movement? Your toes should be rotated outward about 30 degrees, and you need to actively keep your knees out to the sides to track the angle of your toes. Does this happen? It's quite common for people to either hold their toes too straight, or for them to allow their knees to cave towards the middle, especially with heavier weight.
The other question is, do your knees keep traveling forward as your approach parallel, and once you go below? Your knees should assume their final position in the first 1/3-1/2 of the descent, and should stay there.
Have you read Starting Strength by Rippetoe? I would highly advice you do that, especially since you have knee pain.
Also, be careful with the trainers out there, the majority are fools. I've seen countless trainers at typical commercial gyms give just terrible advice. Educate yourself first, and then get a qualified (you'll be able to discern what this entails better once you have some knowledge on form under your belt) coach if you need to.