While pt for herniated disks provide some daily relief, every morning i wake up with a stiff neck negating the pt benefit.what can i do ?

Not negating: You are not negating the pt effect. It is very common to be stiff in the morning if you have back troubles. I have not found a good solution for morning stiffness, although some people find that if they take a hot bath at night before bed, they do better. Also, doing some gentle stretches in bed may help. Talk with your pt.

Sleeping habits: Yes, sleeping positions and pillow conditions can negate all pt and medical help. Try an orthopaedic non allergenic pillow.