You can if you add a scaler between your XGA output and the ATEM. As the others have mentioned, the ATEM wants either 1080i or 720p with no exceptions. XGA is 1024x768 so it won't work out of the box.
A box like this
http://www.markertek.com/Video-Equipmen ... D550.xhtml for $250 will take an HDMI input at whatever resolution (XGA for example) and scale it to 1080i for you. I have not tested this box with the ATEM and it is possible that the HDMI output will not handshake correctly with the ATEM. I have tried this box:
http://www.markertek.com/Video-Equipmen ... 0VGA.xhtml which takes a VGA input and scales it to a 1080i HDMI output and have found that it does not work with the ATEMs, so make sure you're able to return the unit in case it doesn't play nice.
Your other option is to set the output resolution of your computer to the same input resolution of your ATEM (1080i or 720p). Most PowerPoint or presentation software will scale correctly. If you're running this through a projector and hitting a screen, you can have the black bars just shoot off the screen so you don't pillarbox and letterbox the image. Or find a way to cover the black shooting from the sides.
Thanks,
Benjamin
PS - I have stopped linking to B&H because I'm sick of them being closed for 1/2 the year. I personally won't give them any more business, but you're free to check there too.