I did some fiddling around - changing which display was main display and that did nothing but - I did something that "fixed" it - I changed the resolution of the display to the left (the larger display) to be smaller than the display on the right - once I did that I could set the iPad to be arranged below the display on the right - but now I can't place the iPad below the display on the left in the arrange pane. I don't know why this is though, it could be some sort of defect?
Also when I change the resolutions of the monitors in the displays setting pane iPad jumps beneath whichever display has a larger resolution. Weird.
*edit - I am also using DisplayLink for the display to the left which may somehow impact this. So that display is some sort of RemoteDesktop hack built by DisplayLink.