If you are having pain in the top of your foot only when you are wearing shoes, you are probably irritating the nerve on the top of your instep with your shoes. Many people have a prominance in this area due to a high arch and this rubs on their shoes and pinches the nerve causing a burnong pain in the area.
The quick fix to this problem is to loosen your shoes. Padding the area can be helpful. Stop wearing clog-like shoes if you do. If you are still having pain, an injection may be necessary to calm down the nerve. Orthotics may also be necessary to stop excessive motion in the area.