I am not totally familiar with the ultrasound protocols. However, if you still have symptoms then I would not hesitate to go back to the doctor and perhaps a repeat ultrasound would deliver additional information.
The scrotal ultrasound sees the entire testicle (front, back, and sides), even though the probe is only on one side.
The scrotal ultrasound tries to image as much of the epididymis as possible, typically focusing on the head which is usually the most obvious. The body and tail may be more conspicuous if abnormal (e.g., epididymitis).