You can do it all at once. They will get it figured out. The foragers coming back will be a little confused but they will figure it out.
My girls are new and after I took my top feeder if I put in an inner cover and propped up the telescoping top (my inner doesn't have a notch, yet). I didn't reduce the lower, but I don't think I saw a single bee using the top. Though the did cling to the top cover through the inner cover.Michael, I did what you suggested. I guess I should have mentioned that this hive has a screened bottom board and is 5 mediums full to the top with bees. Last night when all the bees came home it created such a traffic jam that a lot of bees went under the hive. It is not very cold here so I didn't worry about it. They were still there and alive at 6:00am when I looked. Tonight the same thing started to happen. At about 3:00pm there were many bees under the hive and the landing board was overflowing with bees trying to get in. I felt sorry for them and it looks like were in for some fog / rain so I took the reducer off and hundreds of bees boiled out. Most of the bees that came out were doing what looked to me like orientation flights. After about two hours all the bees including the ones under the hive were inside.
I have not seen one bee use the top entrance yet.
Maybe not so small of an entrance? Solid bottom board?
Any thoughts are greatly appreciated.