In Maryland, we have both upper and lower entrances available to the bees at
all times.   The only exception would be weak colonies during robbing season.
 Some people even create a third entrance between the queen excluder and the
first super during the honey flow.
 
The only disadvantages I have seen to having an upper entrance available at
all times have been 1) robbing access (generally a non-problem it the base
colony is strong), and 2) supersedure queens that appear during the nectar
flow will generally use the top entrance and set up shop in the supers.
 Weekly super inspections generally keep that problem under control.
 
W. G. Miller
Gaithersburg MD