Understood. What you can do, when you on single monitor mode, move those overlapping fences rearrange it, roll it up, create a new Fences desktop page and move some of those fences to your second Fences desktop page. After all is done and as you wanted them to be. Save a layout snapshot for that one. Also, create another snapshot for your multiple monitor mode. So when you on single monitor mode, you just need to do restore layout snapshot to which every mode you need.
Thank you,
Basj,
Stardock Community Assistant