where in the knee is the dull ache? Inside? Under the kneecap? One of the tendons above or below the kneecap?
Generally speaking, the more knees forward position you adopt in the squat, the greater the sheer on your knees. Sitting back and driving with your hips, as opposed to just your knees, will reduce the strain on your knees. The other thing that will kill knees is letting the knees suddenly slide forward at the bottom of the squat. this is basically you relaxing your hamstrings so you can hit depth. Not only can it destabilise the knee, but by making the hamstrings slack you kill hip drive and reduce the amount of weight you can lift.
If you have these form issues, I would recommend getting some neoprene knee sleeves, which can often help with achy knees. Tommy Konos are excellent and cheap. You can get them from Spritcha on this forum.