Two deeps s/b plenty of room. Bees will continue to die throughout winter. While open did you notice amount of capped honey?
Its true, I use a 'notched' inner cover as a top entrance. On top of that I place an 'empty' box that I fill with dry sugar for the winter. The sugar also acts as an absorber of excess moisture. I place 2" rigid insulation on top of the sugar.
With the abnormal weather I've added another ten pounds of sugar to each of my three colonies just last week. With the top box (feed/vent box) there is little disturbance when checking feed stores, just lift, look, dump in some sugar, close back up.