What should I expect during physical therapy for upper trapezius pain?

Less pain. If you are concerned about the effect of physical therapy, then you should have your pain diminished and range of motion restored. As far as modalities that will be used, I suspect you will have massage, stretching, heat/ice application, ultrasound, iontophoresis, may be traction. It all depends on the physical therapist, his experience and comfort level.
Varies. This will vary depending on you therapist. They will likely concentrate on your neck as most trapezial pain comes from cervical pathology. Massage, deep heating, ultrasound, muscle stim, stretching & strengthening exercises, and traction are all common.