You CAN bodybuild and run at the same time, but its not easy. Eat like a horse, get plenty of rest, and try and cut back on the running a bit. You won't be able to look like Arnold, but you WILL be able to look muscular. And with the cardio you are doing, you'll be able to get cut to shreds.
Not much I can suggest for your knees, because I blew both of mine out from running when I was too heavy. Listen to your body, and if they start hurting, rest them up. I was an idiot and would run regardless of the pain, and now I'm paying for it. I can't run for more then 40 minutes without being in pain. I also wouldn't suggest doing the running and weights on the same day. Switch up, one day lift, the next run. Use a simple weight training program that is short, and with lots of compound movements.
And remember, EAT.