Stop using the treadmill, use the row machine or bike instead. Second of all, I squat heavy and my knees hurt when I squat just the bar, I'm not entirely sure it's something that can be avoided, I have someone check my form on squats and deadlift twice a week and its not bad form on my part, but what I really recommend is that you get knee sleeves. I have the Iron Rebel ones, they're pretty good, SBD are also really good but a little more expensive I think. They keep your joints warm so that helps. You want the tightest size you can squeeze your legs into, for me that was a small. So yeah, what I would recommend is stop using the treadmill, have someone check your form, and get knee sleeves. If you don't have someone to look at your form, film yourself squatting, I can look at it and show it to my coach.
How much weight are you doing now, and what is your routine (sets x reps).
If your knees are going in while squatting that could be part of the problem, what I would recommend in that case is getting a hip circle or small elastic band (not one of the huge ones for assisted pullups) doing warmup sets with that on just below your knees, this will force you to push out against the band and keep your knees from going in. Another thing to think about if your knees are going in is to think about screwing your heels into the ground, but that takes a little explaining...it took me a while to get it.
My goal is 275 by the end of the year btw, but I seem to have hit a plateau because all my muscle is posterior. I wish there were a thread for fitness goals here (that I wouldn't need to necro).