Personally, I would cover those holes in the mow floor overhead. Warm air rises and you will lose your heated air up through the holes. Cold air sinks, and that will just filter down to where the birds are.I love my all three of my breeds. I have been doing the deep litter method since I started raising them. In the winter time the chickens get time in the center of the barn. I give them a choice to go outside but rarely do. I have 6 pens inside, each has a heated dish but the broilers have three of them. I mix their bedding twice a day with oats for them to scratch for. Each breeder pen gets at least three hours out in the center. They get out every other day so they all get a turn. Once a week i add some fresh bedding added. I will also add 20 lbs of barn lime to each pen after I remove all the wet spots from the water. I do have a double window fan that circulates the air 24/7 over their heads. Plus I open the area under the doors to allow more air flow if a mild breeze during the day. At night I plug them back up do to predators. I also have holes in the ceiling that lead to the hay loft. I would usually plug them all up to conserve the heat. This year I am keeping them open for more ventilation. I also will be putting some fine mesh over them to prevent anything falling through them like wild pigeon's.