You can only do so much with cleat position. Cycling shoes are notorious for providing little in the way of arch support. That can cause the foot to rotate longitudinally, which in turn causes uneven loading of the knee joint. This is especially true for people with flat feet. In addition, some people need wedges to keep the foot in the right orientation to evenly load the knee. Unfortunately, none of this stuff is particularly easy to figure out without the aid of a pro fitter.