Hello Anil,
I've completed 10 marathons (including Boston) and ran the last 2 since developing chrondomalacia patella (sp?) in my right knee. I'm not currently "in-training" but I do still run 10-20 miles per week.
The top of my patella bone occasionally scrapes against the inside of the kneecap and inflames the cartilage there. The more inflamed it is the more it scrapes. It feels like a dull ache under my kneecap that turns into a throbbing pain as it increases in intensity. The pain is usually mild while running, but typically flares up the worst the next day.
If this sounds like it may be the source of your knee pain, you can probably continue to train and run your first marathon with it. But I suggest avoiding hard surfaces (concrete sidewalks), lots of turns, steep hills (especially downhills), and even cutting back slightly on your long distance runs to save yourself for race day.
Anything you can do to strengthen the leg muscles around your knees- calves and quadriceps - by weight exercises without the weight of running - will help reduce the wear and tear on the knee when you do run.
Also, lots of rest and sleep between runs, a fresh pair of running shoes every 400 miles logged for maximum cushioning, and the right pair of running shoes for your biomechanics will go a long way in healing and preventing new or recurring injuries. Also, Cho-Pat is one of a host of sports medicine companies that sells flexible knee braces that allow you to run without re-aggrevating existing injuries.
Finally, plenty of hot reiki energy before and after running directly on the knee has helped me run with and through my chronic knee pain.
Or course, if your knee pain is severe while you run, I suggest you cease your training and refrain from running until you're healed and pain free. No sense aggrevating the injury by running on it. I've had to cancel marathons due to other injuries. It only made finishing the next marathon healthy, even sweeter.
Hope this helps. You also may wish to meditate and ask your spirit guides for personal advice.
Good luck and godspeed ...... ***greenlight***