Regarding the knee, we need a lot more information regarding the type of pain you're experiencing. Where about is the pain? What type of activities make it hurt? Does it hurt more going up or down stairs? Does the pain go away once warmed up? Is it dull or sharp pain?
What does your exercise regime look like? You obviously run and do leg presses, what else? What sort of miles do you do each week? Do you do any other leg exercises beside presses?
The potential problem with leg presses is that it's a very quad dominant exercise, it doesn't do a lot in recruiting the hamstrings or the glutes - so the issue can be if you're only doing leg presses you may develop muscle imbalances, and when these occur in your leg and then pull unevenly on the knee, it may hinder the knee tracking correctly.
If you squat with correct form and below parallel, you equal out the forces on the knee by recruiting the quads, hamstrings, glutes and hips in a balanced manner.
Mark Rippetoe's book, Starting Strength, is the best text I have read on perfecting squat form, though a few sessions with a decent coach will get you squatting well in no time, as the instant feed back of form corrections makes the process much faster and is worth the investment.
Of course your issues may not stem from imbalanced muscle issues, it could have some to do with running form, poor flexibility / mobility. When you run, do you heel strike?