When you position the reference box, the tracker box automatically follows. You can leave the boxes together if you place the reference box in the first or last frame of the clip. However, if you start the analysis on a different frame from where you position the reference box, you should position the tracker box in the first frame of the clip on the pattern you want to track. This way, the Stabilizer knows where to look for the pattern to track when you analyse the clip.
To position the reference and tracker boxes:
(a) Tracker buttons (b) Active button
The reference box changes into a magnifying glass. By default, the tracker box follows the reference box.