You'll want to disable window swapping in your ISBoxer window layout if you're doing this, but the way to do it is create a new IS profile (or use Add Game), then in the IS Configuration window you can select the display. To find the option, it's under Game Configuration, then select your game from the drop-down, select a Profile from the next drop-down, and you'll see the option called "Display selection" which defaults to Application Controlled.