I run a notched inner cover with the rim up if it has a flat side to it. Hole in the middle for a quart jar. If you want an upper entrance just slide the outer cover forward and slid to the rear to close it off.
I believe it is best for the bees to have access to the area between the inner and outer cover for housekeeping, and with an entrance to boot they will go into this area.
I have a decent sized notch in my covers that I push the telescoping cover back against in wintertime. I move it out in the spring -- it does not seal up tight, so I get some ventilation but not a howling blast of cold air through the hive.
I always have plenty of bees up on the top of the inner cover drying honey in the summer, I feel they do better with the extra space. I do have a bee escape hole in the center of the cover.
I firmly believe that a double cover provides better conditions in the winter, only a solid slab of wood or a quilt box is better. Wood absorbs quite a bit of moisture before it shows condensation on the surface, and even if wet is unlikely to drip. I have a 1/2" thick inner cover, a space around 3/4", and then another 1/2" of plywood with about 1/2" of newspaper on top under an aluminum cover. Quite a bit of insulation compared to a migratory cover, and no water at all gets in.
I use notched, ventilation and an added entrance are what enticed me to go that route with my hives. Currently closed since my colonies are new and have yet to establish beyond a single box, but will be handy when they get their population up and we enter the warmer months.
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