This is pretty typical for runners, you might want to consider wrapping them for awhile, either the ace bandages or the one piece ones you can get at wallymart. They are miracle workers. They will support your knees and help them while they heal up, then you can start running slowly again. This is what you would do: put the bandages on when you can, when you're in for the rest of the day, and wear them to bed. As much as you can wear them, do this for a good week, and start strengthening your quads after this, slowly and easy. If you have access to a gym the quad machine would be good or squats with a ball against the wall. Strengthen them slow and easy, as you want the knees to heal.
This will be a test of your patience! If you have any warm water available you could soak in this too, or do some exercises in it. (swimming)
These wraps will really help you if you will wear them consistent, I know it's a pain, but they work. I've had injuries during the years I've taught classes, and I use them when I need to. I've taught classes with both knees wrapped before. Hope this helps.....