I and others here have had trouble with overlapping zones, even when putting them on separate layers. Duane Valencia had a recent post about this problem.
I don't know what your project is but there are some workarounds.
For example with residential I have to do heat/cool area and volume. So I have my overall zones on a separate layer but move them a set distance away from the building so all the other schedules read correctly. When ther e is an update in the footprint, I update the geometry of these zones then move them back away from the main building. Tedious, but not difficult. The zone tags stay by the plan so the numbers are read as needed by the building department and others.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"