Take a look at short article Knee Pain: Treatment Based on Indivual Evidence.

Damien Howell PT, DPT, OCS - www.damienhowellpt.com

I trust the ortho's prognosis for your "runner's knee," but you need   further direction to make  sure it comes true. I've had other knee   problems than that, but the  same rules apply, to discover and modify   the cause of this injury before  aggravating it again. It's not all   about the knee.

You should consult with a  physical  therapist (well versed in sports work) about the  possible causes for  this injury, which  probably involves more than  simple overuse. There  is no doubt an  imbalance in the tension of your  quads and/or pelvic  musculature involved. As Damien often points  out, the amount of sitting  and way you  sit can be to blame. Everything  from your hip rotators to  glutes to flexors (including TFL), and tight  hamstrings (extensors)  needs to be addressed.

Make sure the focus is wide enough  to include the big  picture. If you are prepared with the  proper  assessment and appropriate  exercises during your down-time, you  will  have a better chance of  hitting the ground running, so to speak,   during your successful (and  hopefully shortened) recovery.

Hi,

I am a physical therapist.  Chondromalacia Patella (CMP) is a common yet treatable knee condition.  I would definitely make sure you are treating the entire lower extremity as foot biomechanics and hip strength can play a large role in effictively treating this condition.  Deinitely do not do any activity (including running) that causes pain.  This is not a 'push through it' injury.

For more information about the treatment of CMP you can visit the link below:

http://www.joint-pain-solutions.com/knee-cap-pain.html

Good luck,

~JTrempe PT, ATC