First of all, I assume that by the "first layer of your eye" you mean the cornea. The cornea is the clear part in front of your eye through which you see. It is lined by a thin layer of skin cells. When this layer of cells gets disrupted, it causes a corneal abrasion and is very painful. Over time, the cells regrow and the abrasion heals.
However, there is a condition called recurrent corneal erosion. Sometimes, the cells may heal but they don't set firm "roots" down into the stroma of the cornea. Occasionally, the cells can become disrupted again and it will feel like the original abrasion. This usually occurs when you first wake up and open your eyes. The eyelid sticks to the cells while you are sleeping and can tear them off if they are not firmly attached. This phenomena has been documented as long as 52 years after the initial injury. There are treatments for this, including eyedrops, ointments, micropuncture, laser, etc.
Of course, your symptoms may be from common conditions such as allergies, dry eyes, etc. You should consult an eye doctor.
Hope this helps.