Magnifier Aid allows applying software zoom over an image part. It also can work in combination with Focusing Aid in order to inspect closer the star used for focusing. Some imagers investigate the aberrations in stars during the focusing.
The Magnifier Aid use the common aid behavior in APT- dragging the window and placing the Source frame over the image part that you want to use.
Source
It is a "transparent" window that shows the image under the Magnifier Aid and defines what is the source to be used in the Aid.
When selected the Source will be automatically populated with image in Focusing Aid Source frame. If Focus Aid is not available Magnifier acts like this option is disabled.