Well, my first suggestion would be to simply ensure all of your media is already 800x600 or 400x300 (one or the other.) When you do this, and you understand which actors use the "Default Resolution" parameter, and how the "When combining media..." parameter works, you can be specific about what's happening. (Both of these are in the Video tab of the Preferences).

That being said, if you need to output to two screens from a single movie, I'd make it the proper (1600x800 or 800 x1200) size and use the Chopper actor to split it to the two stages.

I hope that gets you started. If you have any other questions or concerns, please feel free to email me.

Best Wishes,

Mark