I use FancyZones as well but I get annoyed that it doesn't seem to preserve custom layouts between reboots. I have to switch to my layouts manually after every reboot. Have you experienced it too? I am curious about whether it is something on my end or not.
It has a setting to remember. If it does not it means you have a problem with display detections
FancyZones seems to forget currently selected layout every time it is updated and every time a new Windows developer preview is installed. Other than that, it should be exactly as you left it.