When should the change from bottom entrances to top entrances be done, and what is the best method for making the change
I run upper entrances all the time now. Assuming you still have a bottom one, you can just put some 1/4" hardware cloth on the bottom for a mouse guard. When I ran bottom entrances thats what I did.
For a winter upper entrance you can do many things. A notched inner cover works for a top entrance. If your inner cover doesn't have a notch you can cut one.
An Imirie shim (you can buy them from Brushy Mt. or buy Betterbees version or make one) works for a top entrance.
Two tapered shims (cut from wood shingles or bought already cut) can be put with one on each side and a 1/4" or 3/8" (depending on how high the shim is at the front end) piece of wood can be used as a reducer to make that entrance smaller. This can be put under the inner cover or a migratory cover. Or you can put it on top of the inner cover and slide the telescopic cover forward to make a gap in the front.
Or you can drill a hole in the top box a 3/8" hole will let the bees out when the snow blocks the bottom entrance.
Lots of things can work depending on what's handy and what you want to do.
Here's my site with a picture of top entrances with shims under a migratory cover: http://incolor.inetnebr.com/bush/bush_bees.htm