When you draw a zone over another zone in EFD, the new zone automatically sits on top.
To change which zone is on top, select the zone and go to MODIFY > Display Order, then choose an option such as Bring to Front. See Display Order.
Zones always stay underneath everything else, but you can change their order relative to each other.
NOTE: Because of a known bug, overlapping zones sometimes don't show in the right order on Floorplan Live, even when they look right in EFD. You can't fix this yourself. If it happens, please contact us and send your EFD file, and we'll fix it for you.