ISBoxer will move your clients however you have them set up to move in your Window Layout. Your situation is a little different than just having 2 monitors each hooked up to a video card. You'll typically want to set a swap group for each video card and, probably in your case, one of these swap groups will need to cover 2 monitors. I don't think the Window Layout Wizard can do what you're looking for out of the box and you'll need to start with something like this and then manually edit the Window Layout yourself. Lax may be able to give a better answer.
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