Rather than replacing the runs with biking, you might just back off on the running mileage a bit. I would also recommend running as much of your mileage as possible on softer surfaces (paths, cc courses etc.).
Also when you are done running you could ice your knees and lower extremities.
A change in shoes might also be in order. Either the shoes you are currently training in are in need of replacement or the model you wear might not be for your particular biomechanics.
The biking is more likely to add to the irritation you feel in that area rather than alleviate it. If you are having repeated problems with your knees, then I would recommend seeing an athletic trainer or a sports med DR.
Good luck