The weather is cooling down so covering the hive at this time would be ok.
It is important to remove any partially filled supers the are on the top of the hive. Partially filled supers left on top of a hive is a fast way to starve a colony come about Jan. The bees will move up following the honey. If they have the misfortune of moving up into a partially filled box of honey the bees will usually starve after it is gone.
For wintering I always make sure the top box is full of honey, my moisture board is on top the inner cover and my black box with a top entrance is on the hive.