When I started C25K I had bad knee pain and it was so bad I talked to my doctor about it.
Aleve is an over the counter med like tylenol or ibuprofen and its main job is an anti-inflammatory. I was told to take it twice a day, but after a week or so I think my knees were able to repair whatever damage I did and now I only take it after running.
Also, as for stretching, my doctor said I may have had what's called Iliotibial Band Syndrome, and she printed off some stretches from the internet for me to try and they feel great. I realized I was tight in those areas, and I think these have helped with my knee pain too.
http://www.howtostretch.com/iliotibi.htm