I run approximately 6 miles every other day and sometimes a few hours after I run the right side of my right knee starts to ache and have pain in it.?

IT band syndrome. Can cause hip and lateral knee pain running without strong core or hip adductors can cause a pro trainer can help look at stride and gait help you adjust.
IT band bursitis. This sounds like it band bursitis. It is due to friction and overuse of the bursa. This feels like an ache or stabbing pain on the outside of knee. It is often tender directly over the bony prominence of your femur in this area. Treat with change in mileage, change running surface (don't always run on the same side of the road), ice after activity if pain, ibuprofen, it band stretch, injection.