I have severe on side of left foot and underneath for past six weeks two x-rays show nothing any ideas it is worse after I have exercised on it?

Side of foot pain. There are a multitude of conditions , that can cause this pain, tendonitis, stress fracture, entrapped nerves, muscle trauma, capsulitis, etc... And x-rays will not reveal any of these....See a specialist. Further testing such as an MRI or ultrasound may help.
Stress fracture? You may have a stress fracture. This often will not be seen on initial x-rays. An MRI can help make the diagnosis. If it is positive make sure your vitamin d levels are checked.
Foot pain. Most likely things could be plantar fasciitis or achilles tendonitis. These conditions do not show up on an x-ray. Also a stress fracture from repetitive running could be the cause which does not show up on x-rays.