If it's an option, having the primary monitor be the farthest left/up will give you the easiest time. Then you just have to mess with all of the positions.

If you have to have one of the secondary monitors above/the the left, fixing the positions might get very difficult if not impossible.

and any themes that load completely in lsboxes should be very easy to make work. (the boxes will be stuck on the primary monitor, but they won't get messed up)