No problem; use whatever you have available. I use loose hay because that's what's here, but I've used bales too (leaves, cardboard covered in poly etc...).
When using bottom entrances 'exclusivly' you'll have to make certain snow isn't covering their exit throughout winter. Top entrances make a perfect ventilation system IMO and your bees will generally have a way out w/out digging through snow when weather permits. I just cut out a 1 1/2 -2 " notch out of the inner cover, notched side down. Now don't get me started on top entrances :-D There's lots of discussions on the subject in these pages.
Depending on where the empty frames are located, you could place them between existing brood frames which s/b on the bottom, to encourage brood rearing or, a better choice this late is to place them up top and hope your bees fill them up w/ goldenrod honey before cold sets in.