For a single monitor you would simply put in the size that you want for the smaller window in Y2 or Y2 to get an aspect ratio the same for both windows.

Although, I would use them both at the native resolution of your monitor (stacked) and have a videoFX display the background window (your slave) on the forground window (your main) and vis versa. VideoFX has a bunch of options in it as well. Such as allowing mouse click to pass through to the source of the video. Meaning, you can click on the videoFX screen displayed on your main character and it clicks on your slave character. Grant it, I haven't been boxing for very long and even less time using ISBoxer but videoFX has a lot of potential if you play around with it and figure it out.