Re: Warre novice in need of help!
You will want to winter the bees in as small an area as possible and still have enough stores to get them through. Any box that is empty, pull out. I assume you are in Idaho. I do not know how much honey you will need to winter there but a little research should turn up the answer. A warre comb will hold about the same amount of honey as a medium langstroth frame.
When pulling a box, try to lift it on one side gently to see if the combs are attached to the top bars of the box below. Lift it on the side adjacent to the end of the combs. If it is attached you can take a piece of thin wire and work across that side and slowly pull it through the gap between boxes. This will leave some mess on the top bars but it can be cleaned up fairly quickly. Sometimes I can avoid all of this by shoving the end of my hive tool under the combs one at a time to break them loose. Little less messy and easier but only works in situations of one or two combs attached.
As this is your colony's first year I would leave all the honey for winter and after the spring flow starts you can take any they haven't used.
I hope this is helpful.
Herbhome Farm USDA zone 7a