The "Bounds" section on the edit screen is what sets the location and size of the windows. You can either manually adjust it to something specific, or you can place the window where you would like it, edit your entry, and drag the blue crosshair over that window to auto select the size and location.

Hope that helps!

Those bounds also decide what monitor the window will move to. DisplayFusion reads the resolution of all your monitors in 1 giant box, with the top left corner of your primary monitor being 0,0. Depending on where the window is relative to that 0,0 location, it will move the window to the monitor with those bounds.

Hope that clears things up!