Hello,
Sorry to hear you are having issues. You can send everything inside a Fences so that it wil never be cover up by Fences. You can do this by create a new Fences and set that fences rule so that all new icons/program than sent to Desktop be send automatically into that Fences. You can manually move those icons to any other Fences from there.

Thanks
Basj,
Stardock Community Assistant.