Mike and my fellow beekeepers:
 
When I seal the joints in an inner cover for ant control,  I seal the joint
between the plywood (or Masonite) and the inner cover's outer rim.   That's
where the ants live.   I most definitely do not block the ventilation out of
the top of the hive.  In fact the rims of all my inner covers have about a 1"
notch to provide increased ventilation and an upper entrance.
 
W. G. Miller
Gaithersburg, MD