You should be able to click the capture window and have a red border show up, you can move that to re scale where the capture is in the view. I only tried this with "Display Capture", not "Game Capture", so it might work differently for you.You can also use this to have a web camera capture in the corner if you want.
Just use desktop capture or whatever so it captures your whole screen.
In your video settings have you checked that your canvas resolution and output resolutions are correct?