This is excerpted from a recent article titled "Spare The Neck: Strengthen the Shoulders and Back" and relates to your question:
"New research published in the journal Arthritis and Rheumatism indicates that strength conditioning may help ease chronic neck and shoulder pain, a problem that has escalated as more and more of us spend increasing amounts of time on our computers. The study included 48 Danish women with chronic trapezius pain, most of whom spent a good part of their workday at their computer. Neck and shoulder pain often stem from the upper trapezius muscle - spanning from the upper back and shoulders - which helps the neck to move. Performing repeated "monotonous" tasks, including typing at a computer keyboard and looking at the monitor can create a tight and tender trapezius muscle."
In my experience with neck tension, it is important to be careful not to overly focus on the area that is "sore" since most often the pain is a symptom of what is going on around it. The Pilates system allows us to treat the body from a holistic standpoint instead isolating a single area. Plan your session incorporating the reformer, mat and reserve time for the Cadillac, barrels and accessories like the arms weight series and ped-a-pull. You may not be able to incorporate every appartus in one session so you can spread it out over the course of several sessions and see what really hits the spot. I find working with predesigned sequences that stretch and strengthen on different apparatus to be most effective, only after I have gone through at least the basic reformer. The key is to work on connecting the arms to the back every time the arms move. Most often, clients with neck issues lift their arms with their trapezius.
By all means keep your client comfortable by using a cervical pillow and give some neck turns as needed for release. That said, the following reformer exercises help strengthen the neck, shoulders and back: Reach and Pull, Rowing, Shave and Hug, Pulling Straps I and II, Short Box Series (hands behind head for sides, flat and twist), Long Stretch, Down Stretch, Stomach Massage Series and Knee Stretch Series. On the Cadillac: Chest Expansion, Supine Reach and Pull, Circles, Triceps; Long Back Stretch Arms, Boxing, Side Pull, and traditional ending. On the Low Barrel: Straight Arm Stretch, Circles. The Ped-a-Pull exercises.
This is just to get you thinking and is by no means intended to identify all the possible exercises that could be helpful. Keep alignment a top priority and remember that there is no one simple answer. Good luck.