I have an arch in my foot but still feel pain in my ankles and knees when i run. any advice/suggestions?

Need more support: You likely need a better support. You should see a podiatrist to get orthotics. You may need firmer support or better control at the heel (heel post).

Have it evaluated.: Your pain could due to trauma (fracture, sprain, arthritis, inflammation), infection, metabolic conditions (gout), poor circulation, musculoskeletal or biomechanical abnormality and different neurologic conditions (neuropathy). A thorough history and physical exam and possibly some laboratory and radiology exams are needed to determine the exact cause. The treatment varies depending on the cause.