[When I first put them on the foragers were using both entrances but now they are only using the bottom.]
It depends on what is being brought in and where it is needed.
Pollen maybe brought in on the lower and nectar might be brought in on the top.
I have seen a change sometimes between entrance choice as the foraging population 'turns over'.
I also see it depends on the colony.
I have some that rather use a hole in the super over either entrance.
I agree on improving ventilation.
I don't like competing with foragers waiting to get into a hive when I am working a hive.
So I don't exactly promote upper entrances as an exclusive entrance.
I also think its a bit cruel to make the hive carry debris to the cover to clean itself.
Screen bottom boards help, but things can grossly pile up in cold spells.
Naturally, I think openings are utilized at all heights (you use what you can get).
I just feel that lower openings allow for better sanitation with the least effort.
I also feel it keeps forager traffic at a location that miminally impacts my inspections.
My experience with upper entrances also concludes that notched inner covers and telescoping covers do not provide as much ventilation as the bees could use. Its probably better than what they get in a tree, but I think that's a low expectation.
-Jeff