You're right to be concerned about correct placement of the pins. During the operation an axis pin is used to guide the location of the fixator pins. The axis pin is put in place parallel to the axis of the joint. The axis is the central point around which the bones on each side of the joint move. It doesn't actually go through the joint itself.
Using the axis pin as a guide, smaller half pins are placed on either side. These are called fixator pins. Once all the connections are made and are secure, the axis pin is taken out.
With a hinged elbow external fixator the pins follow the same axis of joint rotation. In the elbow this axis is straight across but slightly tilted or angled. You should see the pin on the outside of the elbow is slightly lower on the forearm compared to the pin on the inside (medial) of the elbow.
The surgeon uses a special form of X-ray called fluoroscopy to advance the pin into the bone. Careful measurements are taken to make sure there is a proper position. Some slight variation may occur from patient to patient as the surgeon avoids putting the pin through the nerves located on either side of the elbow.