If the 'Show webcam window while recording’ option was enabled when the movie was recorded by Flashback Pro, the webcam window is captured as part of the screen instead of being recorded separately and then layered on to of the screen recording. In this case you will need to set the size and position of the webcam window before you record.
However, by default the 'Show webcam window while recording’ option will not be enabled so the webcam will be saved as a separate layer and you can re-size it or change its position afterwards.