if you want the Window Layout Wizard to use specific monitors for the layout, and also set the preferred order, then you need to set them in the Monitors Collection in the right options (if you select this it will have an ellipsis button which I can't get to show for this screenshot).
For your stacked layout, there is a Stacked option. You could select that as your base layout, then manually update the config afterwards once created, to add in the setup on the second monitor and setup all the VideoFX that you are after.
If you let it create a VideoFX layout by setting the "Use Video FX" option to true, then you can just select a layout how you want it to work (e.g.. Multimonitor, Main on Display1, Smalls on Display2, Avoid Taskbar) , and the layout will take care of the small viewers being on a DXNothing (i.e. it should just give you what you are trying to achieve) and it will automatically stack the games all on the main display.
For a matching 16:9 ratio, 1920x1080 = 1680x945, so there will always be a bit of a difference somewhere. VideoFX may fill that in, or more likely it will letterbox it and you will have black bars.
p.s. You should set the options on the right first, then select a Layout from the drop down.