With SE, all rendering happens in the stage window, and it's WYSIWYG. Unless your desktop resolution is larger than the output resolution (the resolution of your captured video in this case) you won't be able to do it in SE.
There are some cases where a workaround is possible (for instance if you're adding an effect that doesn't take up your full frame output size), but it's a little more difficult.
So step 1 is to maximize SE so it fills your desktop. Step 2 is to manually resize the stage window so it can fit your output size (not possible unless your desktop resolution is higher than the output size you want).
Alan.
http://www.wondertouch.com